Plasmodium falciparum antigens and methods of use

ABSTRACT

the subject invention provides novel Plasmodium falciparum antigens and novel polynucleotides encoding these antigens. Also provided by the subject invention are methods of using these antigens and polynucleotides.

CROSS REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application 60/431,494, filed Dec. 6, 2002, which is hereby incorporated by reference in its entirety, including all drawings and tables.

The subject invention was made with government support under a research project supported by Grant No. 1 R43AI49051-01 NIAID.

BACKGROUND OF INVENTION

The recent explosion in genomic sequencing has deposited a wealth of information in the hands of researchers. However, there is not yet a means to efficiently analyze such data to identify which antigens among many thousands are appropriate targets for vaccine development.

More than 5000 proteins are expressed during the life cycle of the Plasmodium spp. parasite. Subunit vaccines currently in development are based on a single or few antigens and may therefore, elicit too narrow a breadth of response, providing neither optimal protection nor protection on genetically diverse backgrounds. By contrast, to duplicate the protection induced by whole organism vaccination (Good, M. F. & Doolan, D. L. Immune effector mechanisms in malaria. Curr. Opin. Immunol. 11, 412-419 (1999)), a malaria vaccine targeting an unprecedented number of parasite-derived proteins through inclusion of their minimal CD8⁺ and CD4⁺ T cell epitopes in a multiepitope construct appears to be required. However, the antigens mediating whole organism induced protection are largely unknown.

Because of various factors, principally related to antigen abundance and immunodominance, not all possible antigens are recognized by natural immunity (Yewdell J W, Bennink J R. Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu. Rev. Immunol. 17, 51-88. (1999)). Various approaches have been proposed for antigen identification, including expression cloning (Kawakami, Y. & Rosenberg, S. A. Immunobiology of human melanoma antigens MART-1 and gp100 and their use for immuno-gene therapy. Int. Rev. Immunol. 14, 173-192 (1997)), elution and mass spectrometry sequencing of naturally processed MHC-bound peptides (Rotzschke, O. et al. Isolation and analysis of naturally processed viral peptides as recognized by cytotoxic T cells. Nature 348, 252-254 (1990); van Bleek, G. M. & Nathenson, S. G. Isolation of an endogenously processed immunodominant viral peptide from the class I H-2 Kb molecule. Nature 348, 213-216 (1990); Hunt, D. F. et al. Peptides presented to the immune system by the murine class II major histocompatibility complex molecule I-Ad. Science 256, 1817-1820 (1992); Cox, A. L. et al. Identification of a peptide recognized by five melanoma-specific human cytotoxic T cell lines. Science 264, 716-719 (1994)), in vitro testing of pools of overlapping peptides (Kern, F. et al. Cytomegalovirus (CMV) Phosphoprotein 65 Makes a Large Contribution to Shaping the T Cell Repertoire in CMV-Exposed Individuals. J. Infect. Dis. 185, 1709-1716 (2002)), and reverse immunogenetics (Davenport, M. P. & Hill, A. V. Reverse immunogenetics: from HLA-disease associations to vaccine candidates. Mol. Med. Today 2, 38-45 (1996); Aidoo, M. et al. Identification of conserved antigenic components for a cytotoxic T lymphocyte-inducing vaccine against malaria. Lancet 345, 1003-1007 (1995)). However, these methods suffer from potential problems such as the repeated identification of the same (frequent/dominant) epitope, biases at the level of expansion of T cell populations, and use of clonal/oligoclonal T cells. They also tend to underestimate the complexity of responses, and are not able to analyze a large number of potential targets in the context of multiple HLA types. Finally, none of these approaches easily lends itself towards the daunting task of efficiently analyzing large amounts of genomic sequence data.

BRIEF SUMMARY

The subject invention also provides novel Plasmodium falciparum antigens that are useful in therapeutic and diagnostic applications. In various aspects, the subject invention provides embodiments such as:

A) isolated and/or purified polynucleotide sequences comprising:

-   -   a) a polynucleotide sequence encoding a polypeptide sequence         selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5,         6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,         23, 24, 25, 26, and 27;     -   b) a complementary polynucleotide sequence to a polynucleotide         sequence encoding a polypeptide sequence selected from the group         consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,         13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27;     -   c) a polynucleotide sequence having at least about 20% to 99.99%         identity to a polynucleotide sequence of A(a) or A(b);     -   d) a fragment of a polynucleotide sequence according to A(a) or         A(b);     -   e) a polynucleotide sequence encoding a polypeptide as set forth         in Table 2, 3, 4, 5, or 6, or a polynucleotide sequence encoding         a polypeptide selected from the group consisting of SEQ ID NO:         1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,         19, 20, 21, 22, 23, 24, 25, 26, and 27;     -   f) a polynucleotide sequence encoding a variant of a polypeptide         (e.g., a variant polypeptide) selected from the group consisting         of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,         16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27;     -   g) a polynucleotide sequence encoding a polypeptide fragment of         a polypeptide selected from the group consisting of SEQ ID NO:         1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,         19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment has         substantially the same serologic reactivity as the native         polypeptide and/or substantially the same T-cell reactivity as         the native polypeptide or fragment;     -   h) a polynucleotide sequence encoding a fragment of a variant         polypeptide of a polypeptide selected from the group consisting         of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,         16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the         fragment of the variant polypeptide has substantially the same         serologic activity as the native polypeptide or substantially         the same T-cell reactivity as the native polypeptide or         fragment; or     -   i) a polynucleotide sequence encoding a multi-epitope construct;

B) primers or detection probes (e.g., fragments of the disclosed polynucleotide sequences) for hybridization with a target sequence or the amplicon generated from the target sequence comprising a sequence of at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 consecutive nucleotides of the polynucleotide sequences set forth herein. Labeled probes or primers are labeled with a radioactive compound or with another type of label as set forth in embodiment C, below;

C) isolated polynucleotides according to embodiments A or B further comprising a label; labels can include, and are not limited to 1) radioactive labels, 2) enzyme labels, 3) chemiluminescent labels, 4) fluorescent labels, 5) magnetic labels, or other suitable labels. Exemplary labels include, and are not limited to, ³²P, ³⁵S, ³H, ¹²⁵I, biotin, acetylaminofluorene, digoxigenin, 5-bromo-deoxyuridine, or fluorescein;

D) methods of detecting P. falciparum in biological samples comprising contacting a biological sample with isolated polynucleotides of embodiments A, B, or C. In this embodiment, P. falciparum cells, or cells comprising (infected) by P. falciparum are recovered, lysed, and DNA and/or RNA are extracted from the lysed cells. The extracted DNA or RNA is then tested using polynucleotides and/or probes set forth herein for the presence of P. falciparum. Typical assay formats utilizing nucleic acid hybridization includes, and are not limited to, 1) nuclear run-on assay, 2) slot blot assay, 3) northern blot assay (Alwine, et al. Proc. Natl. Acad. Sci. 74:5350), 4) magnetic particle separation, 5) nucleic Acid or DNA chips, 6) reverse Northern blot assay, 7) dot blot assay, 8) in situ hybridization, 9) RNase protection assay (Melton, et al. Nuc. Acids Res. 12:7035 and as described in the 1998 catalog of Ambion, Inc., Austin, Tex.), 10) ligase chain reaction, 11) polymerase chain reaction (PCR), 12) reverse transcriptase (RT)-PCR (Berchtold, et al. Nuc. Acids. Res. 17:453), 13) differential display RT-PCR (DDRT-PCR) or other suitable combinations of techniques and assays;

E) analytical systems, such as DNA chips comprising polynucleotide sequences according to embodiments A, B, or C;

F) modified polynucleotide sequences comprising polynucleotide sequences according to embodiments A or B;

G) a polynucleotide sequence according to embodiments A, B, or F, further comprising regulatory sequences, such as promoters, enhancer elements, or termination sequences, that are operably linked to the polynucleotide sequences of embodiments A or B;

H) a vector comprising a promoter operably linked to a nucleic acid sequence of the subject invention (e.g., as set forth in embodiments A, B, or F), optionally, one or more origins of replication, and, optionally, one or more selectable markers (e.g., an antibiotic resistance gene);

I) host cells transformed by a vector according embodiment G or H. The host cell may be chosen from eukaryotic or prokaryotic systems, such as for example bacterial cells, (Grain negative or Gram positive), yeast cells, animal cells (such as Chinese hamster ovary (CHO) cells), plant cells, and/or insect cells using baculovirus vectors. In some embodiments, the host cells for expression of the polypeptides include, and are not limited to, those taught in U.S. Pat. Nos. 6,319,691, 6,277,375, 5,643,570, or 5,565,335, each of which is incorporated by reference in its entirety, including all references cited within each respective patent.

I) novel compositions comprising a pharmaceutically acceptable carrier and a polynucleotide according to embodiments A or B;

J) methods of inducing an immune response or protective immune response in an individual comprising the administration of a composition comprising a polynucleotide according to embodiments A and/or B and a pharmaceutically acceptable carrier in an amount sufficient to induce an immune response;

K) the method according to embodiment J, further comprising the administration of: 1) a viral vector comprising a polynucleotide according to embodiment A and/or B (or composition comprising the viral vector); and/or 2) a polypeptide antigen (or composition thereof) of the invention; in a preferred embodiment, the antigen is the polypeptide that is encoded by the polynucleotide administered as the polynucleotide vaccine. As a particularly preferred embodiment, the polypeptide antigen is administered as a booster subsequent to the initial administration of the polynucleotide vaccine. Exemplary viral vectors suitable for use in this embodiment include, but are not limited to, poxvirus such as vaccinia virus, avipox virus, fowlpox virus, a highly attenuated vaccinia virus (such as Ankara or MVA [Modified Vaccinia Ankara]), retrovirus, adenovirus, baculovirus and the like. In a preferred embodiment, the viral vector is Ankara or MVA;

L) compositions comprising the polynucleotides of embodiments A, B, or F inserted into nucleic acid vaccine vectors (plasmids) or viral vectors and, optionally, a pharmaceutically acceptable carrier, e.g., saline;

M) one or more isolated polypeptides comprising:

-   -   a) a polypeptide encoded by a polynucleotide sequence according         to embodiment A(a);     -   b) a variant polypeptide encoded by a polynucleotide sequence         having at least about 20% to 99.99% identity to a polynucleotide         according to embodiment A(a);     -   c) a fragment of a polypeptide or a variant polypeptide, wherein         said fragment or variant has substantially the same serologic         reactivity or substantially the same T-cell reactivity as the         native polypeptide (e.g., those polypeptides set forth in SEQ ID         NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,         18, 19, 20, 21, 22, 23, 24, 25, 26, 27 and Tables 2, 3, 4, 5 or         6);     -   d) a polypeptide sequence provided in Tables 2, 3, 4, 5 or 6 or         selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4,         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, and 27;     -   e) a variant polypeptide having at least about 20% to 99.99%         identity to a polypeptide provided in Tables 2, 3, 4, 5 or 6 or         selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4,         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, and 27;     -   f) a polypeptide (epitope) set forth in Table 2, 3, 4, 5 or 6;         or     -   g) a multi-epitope construct: 1) comprising at least one epitope         set forth in Table 2, 3, 4, 5 or 6; 2) comprising a polypeptide         selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4,         5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,         22, 23, 24, 25, 26, and 27 and at least one epitope set forth in         Tables 2, 3, 4, 5 and/or 6; or 3) comprising and at least one         epitope set forth in Tables 2, 3, 4, 5 and/or 6 and one or more         polypeptide selected from the group consisting of SEQ ID NO: NO:         1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,         19, 20, 21, 22, 23, 24, 25, 26, and 27;

N) a polypeptide epitope according to embodiment M(f), wherein the polypeptide epitope is a CTL-inducing peptides of about 13 residues or less in length, preferably between about 8 and about 11 residues (e.g., 8, 9, 10 or all residues), and more preferably 9 or 10 residues;

O) a polypeptide epitope according to embodiment M(f), wherein the polypeptide epitope is a HTL-inducing peptide of less than about 50 residues, preferably, between about 6 and about 30 residues, more preferably, between about 12 and 25 residues (e.g., 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 residues), and most preferably, between about 15 and 20 residues (e.g., 15, 16, 17, 18, 19, or 20 residues);

P) methods for eliciting an immune response in an individual comprising the administration of compositions comprising polypeptides according to embodiment M or N to an individual in amounts sufficient to induce an immune response in the individual;

Q) a composition comprising a pharmaceutically acceptable carrier and a polypeptide according to embodiment M or N, that can, optionally, contain an adjuvant;

R) diagnostic assays based upon Western blot formats, or standard immunoassays known to the skilled artisan, comprising contacting a biological sample obtained from an individual with a polypeptide according to the embodiments M or N and detecting the formation of an antibody-antigen complex or detecting the stimulation of T-cells obtained from the individual (for example, as set forth in the Examples herein);

S) a “multi-epitope construct” comprising: 1) polynucleotides that encode multiple polypeptide epitopes (of any length) that can bind to one or more molecules functioning in the immune system; or 2) polypeptides comprising multiple polypeptide epitopes that can bind to one or more molecules functioning in the immune system. Some embodiments provide for “multi-epitope constructs” that comprise a combination or series of different epitopes, optionally connected by “flanking” residues. “Multi-epitope constructs” can include the full length polypeptides from which the epitopes are obtained (e.g., the polypeptides of SEQ ID NOs: 1-27);

T) a multi-epitope construct according to embodiment S, wherein the epitopes used in the formation of the multi-epitope construct are selected from those set forth in Table 2, Table, 3, Table 4, Table 5, and Table 6;

U) a multi-epitope construct according to embodiments S or T that is of “high affinity” or “intermediate affinity”;

V) a multi-epitope construct according to embodiments S, T, or U that comprises five or more, ten or more, fifteen or more, twenty or more, or twenty-five or more epitopes. Other embodiments provide multi-epitope constructs that comprise at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 epitopes.

W) a multi-epitope construct according to embodiments S, T, U, or V wherein: a) all of the epitopes in a multi-epitope construct are from one organism (e.g., the epitopes are obtained from P. falciparum); or b) or the multi-epitope construct includes epitopes present in two or more different organisms (e.g., some epitopes from P. falciparum and some epitopes from another organism). Additionally, the same epitope may be present in a multi-epitope construct at more than one location in the construct. In some embodiments, novel epitopes of the subject invention may be linked to known epitopes of an organism (e.g., P. falciparum or another organism).

X) a multi-epitope construct according to embodiments S, T, U, V, or W, wherein the individual epitopes interact with an antigen binding site of an antibody molecule or fragment thereof, a class I HLA, a T-cell receptor, and/or a class II HLA molecule.

Y) a multi-epitope construct according to embodiments S, T, U, V, W, or X, wherein the construct further comprises, optionally, 1 to 5 “flanking” or “linking” residues positioned next to one or more epitopes;

Z) a multi-epitope construct according to embodiments S, T, U, V, W, X, or Y that has, optionally, been “optimized”;

AA) an isolated antibody or fragment thereof that specifically binds to a polypeptide as set forth in embodiments M or N;

BB) a viral vector comprising a polynucleotide according to embodiment A or B. Exemplary viral vectors suitable for use in this embodiment include, but are not limited to, poxvirus such as vaccinia virus, avipox virus, fowlpox virus, a highly attenuated vaccinia virus (such as Ankara or MVA [Modified Vaccinia Ankara]), retrovirus, adenovirus, baculovirus and the like. In a preferred embodiment, the viral vector is Ankara or MVA; and/or

CC) a viral vector according to embodiment BB, wherein the viral vector further comprises nucleic acids encoding immunostimulatory molecules such as IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-15, Il-16, Il-18, IL-23, IL-24, erythropoietin, G-CSF, M-CSF, platelet derived growth factor (PDGF), MSF, FLT-3 ligand, EGF, fibroblast growth factor (FGF; e.g., aFGF (FGF-1), bFGF (FGF-2), FGF-3, FGF4, FGF-5, FGF-6, or FGF-7), insulin-like growth factors (e.g., IGF-1, IGF-2); vascular endothelial growth factor (VEGF); interferons (e.g., IFN-γ, IFN-α, IFN-β); leukemia inhibitory factor (LIF); ciliary neurotrophic factor (CNTF); oncostatin M; stem cell factor (SCF); transforming growth factors (e.g., TGF-α, TGF-β1, TGF-β1, TGF-β1), or chemokines (such as, but not limited to, BCA-1/BLC-1, BRAK/Kec, CXCL16, CXCR3, ENA-78/LIX, Eotaxin-1, Eotaxin-2/MPIF-2, Exodus-2/SLC, Fractalkine/Neur7otactin, GROalpha/MGSA, HCC-1, I-TAC, Lymphotactin/ATAC/SCM, MCP-1/MCAF, MCP-3, MCP4, MDC/STCP-1, ABCD-1, MIP-1α, MIP-1β, MIP-2α/GROβ, MIP-3α/Exodus/LARC, MIP-3β/Exodus-3/ELC, MIP-4/PARC/DC-CK1, PFA, RANTES, SDF1α, TARC, or TECK).

BRIEF DESCRIPTION OF DRAWINGS AND TABLES

Table 1 presents a summary of immune reactivities of a panel of 27 novel antigens and four known antigens.

Tables 2-6 provide peptide epitopes of P. falciparum.

BRIEF DESCRIPTION OF SEQUENCES

Sequence ID NOs: 1-27 are amino acid sequences of novel malaria antigens.

DETAILED DISCLOSURE

The subject invention provides isolated and/or purified novel P. falciparum polynucleotides and fragments of these novel polynucleotides. Thus, the present invention provides isolated and/or purified polynucleotide sequences comprising:

-   -   a) a polynucleotide sequence encoding a polypeptide sequence         selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5,         6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,         23, 24, 25, 26, and 27;     -   b) a complementary polynucleotide sequence to a polynucleotide         sequence encoding a polypeptide sequence selected from the group         consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,         13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27;     -   c) a polynucleotide sequence having at least about 20% to 99.99%         identity to a polynucleotide sequence of (a) or (b);     -   d) a fragment of a polynucleotide sequence according to (a) or         (b);     -   e) a polynucleotide sequence encoding a polypeptide as set forth         in Table 2, 3, 4, 5 or 6 or a polynucleotide sequence encoding a         polypeptide selected from the group consisting of SEQ ID NO: 1,         2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,         20, 21, 22, 23, 24, 25, 26, and 27;     -   f) a polynucleotide sequence encoding variant of a polypeptide         (e.g., a variant polypeptide) selected from the group consisting         of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,         16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27;     -   g) a polynucleotide sequence encoding a polypeptide fragment of         a polypeptide selected from the group consisting of SEQ ID NO:         1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,         19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment has         substantially the same serologic reactivity as the native         polypeptide or substantially the same T-cell reactivity as the         native polypeptide or fragment;     -   h) a polynucleotide sequence encoding a fragment of a variant         polypeptide of a polypeptide selected from the group consisting         of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,         16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the         fragment of the variant polypeptide has substantially the same         serologic activity as the native polypeptide or substantially         the same T-cell reactivity as the native polypeptide or         fragment; or     -   i) a polynucleotide sequence encoding a multi-epitope construct.

“Nucleotide sequence”, “polynucleotide” or “nucleic acid” can be used interchangeably and are understood to mean, according to the present invention, either a double-stranded DNA, a single-stranded DNA or products of transcription of the said DNAs (e.g., RNA molecules). It should also be understood that the present invention does not relate to genomic polynucleotide sequences of P. falciparum in their natural environment or natural state. The nucleic acid, polynucleotide, or nucleotide sequences of the invention have been isolated, purified (or partially purified), by separation methods including, but not limited to, ion-exchange chromatography, molecular size exclusion chromatography, affinity chromatography, or by genetic engineering methods such as amplification, cloning, subcloning or chemical synthesis.

A homologous polynucleotide or polypeptide sequence, for the purposes of the present invention, encompasses a sequence having a percentage identity with the polynucleotide or polypeptide sequences, set forth herein, of between at least (or at least about) 20.00% to 99.99% (inclusive). The aforementioned range of percent identity is to be taken as including, and providing written description and support for, any fractional percentage, in intervals of 0.01%, between 20.00% and, up to, including 99.99%. These percentages are purely statistical and differences between two nucleic acid sequences can be distributed randomly and over the entire sequence length.

In various embodiments, homologous sequences can exhibit a percent identity of 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent with the sequences of the instant invention. Typically, the percent identity is calculated with reference to the full length, native, and/or naturally occurring polypeptide or polynucleotide (e.g., those polypeptides set forth in SEQ ID NOs: 1 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 or those set forth in SEQ ID NOs:28-81)). The terms “identical” or percent “identity”, in the context of two or more polynucleotide or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithm or by manual alignment and visual inspection. Preferably, such a substitution is made in accordance with analoging principles set forth, e.g., in co-pending U.S. Ser. No. 09/260,714 filed Mar. 1, 1999 and U.S. Ser. No. 09/226,775, filed Jan. 6, 1999 and PCT application number PCT/US00/19774 each of which is hereby incorporated by reference in its entirety.

Both protein and nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTA, TFASTA, and CLUSTALW (Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA 85(8):2444-2448; Altschul et al., 1990, J. Mol. Biol. 215(3):403-410; Thompson et al., 1994, Nucleic Acids Res. 22(2):4673-4680; Higgins et al., 1996, Methods Enzymol. 266:383-402; Altschul et al., 1990, J. Mol. Biol. 215(3):403-410; Altschul et al, 1993, Nature Genetics 3:266-272). Sequence comparisons are, typically, conducted using default parameters provided by the vendor or using those parameters set forth in the above-identified references, which are hereby incorporated by reference in their entireties.

A “complementary” polynucleotide sequence, as used herein, generally refers to a sequence arising from the hydrogen bonding between a particular purine and a particular pyrimidine in double-stranded nucleic acid molecules (DNA-DNA, DNA-RNA, or RNA-RNA). The major specific pairings are guanine with cytosine and adenine with thymine or uracil. A “complementary” polynucleotide sequence may also be referred to as an “antisense” polynucleotide sequence or an “antisense” sequence.

Sequence homology and sequence identity can also be determined by hybridization studies under high stringency, intermediate stringency, and/or low stringency. Various degrees of stringency of hybridization can be employed. The more severe the conditions, the greater the complementarity that is required for duplex formation. Severity of conditions can be controlled by temperature, probe concentration, probe length, ionic strength, time, and the like. Preferably, hybridization is conducted under low, intermediate, or high stringency conditions by techniques well known in the art, as described, for example, in Keller, G. H., M. M. Manak [1987] DNA Probes, Stockton Press, New York, N.Y., pp. 169-170.

For example, hybridization of immobilized DNA on Southern blots with ³²P-labeled gene-specific probes can be performed by standard methods (Maniatis et al. [1982] Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York). In general, hybridization and subsequent washes can be carried out under intermediate to high stringency conditions that allow for detection of target sequences with homology to the exemplified polynucleotide sequence. For double-stranded DNA gene probes, hybridization can be carried out overnight at 20-25° C. below the melting temperature (T_(m)) of the DNA hybrid in 6× SSPE, 5× Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. The melting temperature is described by the following formula (Beltz et al. [1983] Methods of Enzymology, R. Wu, L. Grossman and K. Moldave [eds.] Academic Press, New York 100:266-285).

Tm=81.5° C.+16.6 Log[Na⁺]+0.41 (% G+C)−0.6 1 (% formamide)−600/length of duplex in base pairs.

Washes are typically carried out as follows:

(1) twice at room temperature for 15 minutes in 1× SSPE, 0.1% SDS (low stringency wash);

(2) once at T_(m)−20° C. for 15 minutes in 0.2× SSPE, 0.1% SDS (intermediate stringency wash).

For oligonucleotide probes, hybridization can be carried out overnight at 10-20° C. below the melting temperature (T_(m)) of the hybrid in 6× SSPE, 5× Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. T_(m) for oligonucleotide probes can be determined by the following formula:

T_(m) (° C.)=2(number T/A base pairs)⁺4(number G/C base pairs) (Suggs et al. [1981] ICN-UCLA Symp. Dev. Biol. Using Purified Genes, D. D. Brown [ed.], Academic Press, New York, 23:683-693).

Washes can be carried out as follows:

(1) twice at room temperature for 15 minutes 1× SSPE, 0.1% SDS (low stringency wash);

2) once at the hybridization temperature for 15 minutes in 1× SSPE, 0.1% SDS (intermediate stringency wash).

In general, salt and/or temperature can be altered to change stringency. With a labeled DNA fragment >70 or so bases in length, the following conditions can be used: Low: 1 or 2X SSPE, room temperature Low: 1 or 2X SSPE, 42° C. Intermediate: 0.2X or 1X SSPE, 65° C. High: 0.1X SSPE, 65° C.

By way of another non-limiting example, procedures using conditions of high stringency can also be performed as follows: Pre-hybridization of filters containing DNA is carried out for 8 h to overnight at 65° C. in buffer composed of 6× SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA. Filters are hybridized for 48 h at 65° C., the preferred hybridization temperature, in pre-hybridization mixture containing 100 μg/ml denatured salmon sperm DNA and 5-20×10⁶ cpm of ³²P-labeled probe. Alternatively, the hybridization step can be performed at 65° C. in the presence of SSC buffer, 1×SSC corresponding to 0.15M NaCl and 0.05 M Na citrate. Subsequently, filter washes can be done at 37° C. for 1 h in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and 0.01% BSA, followed by a wash in 0.1×SSC at 50° C. for 45 min. Alternatively, filter washes can be performed in a solution containing 2×SSC and 0.1% SDS, or 0.5×SSC and 0.1% SDS, or 0.1×SSC and 0.1% SDS at 68° C. for 15 minute intervals. Following the wash steps, the hybridized probes are detectable by autoradiography. Other conditions of high stringency which may be used are well known in the art and as cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. are incorporated herein in their entirety.

Another non-limiting example of procedures using conditions of intermediate stringency are as follows: Filters containing DNA are pre-hybridized, and then hybridized at a temperature of 60° C. in the presence of a 5×SSC buffer and labeled probe. Subsequently, filters washes are performed in a solution containing 2×SSC at 50° C. and the hybridized probes are detectable by autoradiography. Other conditions of intermediate stringency which may be used are well known in the art and as cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y. are incorporated herein in their entirety.

Duplex formation and stability depend on substantial complementarity between the two strands of a hybrid and, as noted above, a certain degree of mismatch can be tolerated. Therefore, the probe sequences of the subject invention include mutations (both single and multiple), deletions, insertions of the described sequences, and combinations thereof, wherein said mutations, insertions and deletions permit formation of stable hybrids with the target polynucleotide of interest. Mutations, insertions and deletions can be produced in a given polynucleotide sequence in many ways, and these methods are known to an ordinarily skilled artisan. Other methods may become known in the future.

It is also well known in the art that restriction enzymes can be used to obtain functional fragments of the subject DNA sequences. For example, Bal31 exonuclease can be conveniently used for time-controlled limited digestion of DNA (commonly referred to as “erase-a-base” procedures). See, for example, Maniatis et al. [1982] Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York; Wei et al. [1983] J. Biol. Chem. 258:13006-13512.

The present invention further comprises fragments of the polynucleotide sequences of the instant invention. Representative fragments of the polynucleotide sequences according to the invention will be understood to mean any nucleotide fragment having at least 8 successive nucleotides, preferably at least 12 successive nucleotides, and still more preferably at least 15 or at least 20 successive nucleotides of the sequence from which it is derived. The upper limit for such fragments is the total number of polynucleotides found in the full length sequence (or, in certain embodiments, of the full length open reading frame (ORF) identified herein).

In some embodiments, the subject invention includes those fragments capable of hybridizing under various conditions of stringency conditions (e.g., high or intermediate or low stringency) with a nucleotide sequence according to the invention; fragments that hybridize with a nucleotide sequence of the subject invention can be, optionally, labeled as set forth below.

Other embodiments provide for nucleic acid fragments corresponding to nucleotide sequences comprising full, or partial, open reading frames (ORF sequences). Also within the scope of the invention are those polynucleotide fragments encoding polypeptides reactive with antibodies found in the serum of individuals infected with P. falciparum. Fragments according to the subject invention can be obtained, for example, by specific amplification (e.g., PCR amplification), digestion with restriction enzymes, of nucleotide sequences according to the invention. Such methodologies are well-known in the art and are taught, for example, by Sambrook et al., 1989. Nucleic acid fragments according to the invention can also be obtained by chemical synthesis according to methods well known to persons skilled in the art.

The subject invention also provides nucleic acid based methods for the identification of the presence of an organism in a sample. In these varied embodiments, the invention provides for the detection of nucleic acids in a sample comprising contacting a sample with a nucleic acid (polynucleotide) of the subject invention (such as an RNA, mRNA, DNA, cDNA, or other nucleic acid). In a preferred embodiment, the polynucleotide is a probe that is, optionally, labeled and used in the detection system. Many methods for detection of nucleic acids exist and any suitable method for detection is encompassed by the instant invention. Typical assay formats utilizing nucleic acid hybridization includes, and are not limited to, 1) nuclear run-on assay, 2) slot blot assay, 3) northern blot assay (Alwine, et al. Proc. Natl. Acad. Sci. 74:5350), 4) magnetic particle separation, 5) nucleic Acid or DNA chips, 6) reverse Northern blot assay, 7) dot blot assay, 8) in situ hybridization, 9) RNase protection assay (Melton, et al. Nuc. Acids Res. 12:7035 and as described in the 1998 catalog of Ambion, Inc., Austin, Tex.), 10) ligase chain reaction, 11) polymerase chain reaction (PCR), 12) reverse transcriptase (RT)-PCR (Berchtold, et al., Nuc. Acids. Res. 17:453), 13) differential display RT-PCR (DDRT-PCR) or other suitable combinations of techniques and assays. Labels suitable for use in these detection methodologies include, and are not limited to 1) radioactive labels, 2) enzyme labels, 3) chemiluminescent labels, 4) fluorescent labels, 5) magnetic labels, or other suitable labels, including those set forth below. These methodologies and labels are well known in the art and widely available to the skilled artisan. Likewise, methods of incorporating labels into the nucleic acids are also well known to the skilled artisan.

Thus, the subject invention also provides detection probes (e.g., fragments of the disclosed polynucleotide sequences) for hybridization with a target sequence or the amplicon generated from the target sequence. Such a detection probe will advantageously have as sequence a sequence of at least 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides. Labeled probes or primers are labeled with a radioactive compound or with another type of label as set forth above. Alternatively, non-labeled nucleotide sequences may be used directly as probes or primers; however, the sequences are generally labeled with a radioactive element (³²P, ³⁵S, ³H, ¹²⁵I) or with a molecule such as biotin, acetylaminofluorene, digoxigenin, 5-bromo-deoxyuridine, or fluorescein to provide probes that can be used in numerous applications.

The polynucleotide sequences according to the invention may also be used in analytical systems, such as DNA chips. DNA chips and their uses are well known in the art and (see for example, U.S. Pat. Nos. 5,561,071; 5,753,439; 6,214,545; Schena et al., BioEssays, 1996, 18:427-431; Bianchi et al., Clin. Diagn. Virol., 1997, 8:199-208; each of which is hereby incorporated by reference in their entireties) and/or are provided by commercial vendors such as Affymetrix, Inc. (Santa Clara, Calif.). In addition, the nucleic acid sequences of the subject invention can be used as molecular weight markers in nucleic acid analysis procedures.

The subject invention also provides for modified nucleotide sequences. Modified nucleic acid sequences will be understood to mean any nucleotide sequence that has been modified, according to techniques well known to persons skilled in the art, and exhibiting modifications in relation to the native, naturally occurring nucleotide sequences. One non-limiting example of a “modified” nucleotide sequences includes mutations in regulatory and/or promoter sequences of a polynucleotide sequence that result in a modification of the level of expression of the polypeptide. A “modified” nucleotide sequence will also be understood to mean any nucleotide sequence encoding a “modified” polypeptide as defined below.

Another aspect of the invention provides vectors for the cloning and/or the expression of a polynucleotide sequence taught herein. Vectors of this invention, including vaccine vectors, can also comprise elements necessary to allow the expression and/or the secretion of the said nucleotide sequences in a given host cell. The vector can contain a promoter, signals for initiation and for termination of translation, as well as appropriate regions for regulation of transcription. In certain embodiments, the vectors can be stably maintained in the host cell and can, optionally, contain signal sequences directing the secretion of translated protein. These different elements are chosen according to the host cell used. Vectors can integrate into the host genome or, optionally, be autonomously-replicating vectors.

The subject invention also provides for the expression of a polypeptide, peptide, derivative, or variant encoded by a polynucleotide sequence disclosed herein comprising the culture of an organism transformed with a polynucleotide of the subject invention under conditions that allow for the expression of the polypeptide, peptide, derivative, or analog and, optionally, recovering the expressed polypeptide, peptide, derivative, or analog.

The disclosed polynucleotide sequences can also be regulated by a second nucleic acid sequence so that the protein or peptide is expressed in a host transformed with the recombinant DNA molecule. For example, expression of a protein or peptide may be controlled by any promoter/enhancer element known in the art. Promoters which may be used to control expression include, but are not limited to, the CMV-IE promoter, the SV40 early promoter region (Bernoist and Chambon, 1981, Nature 290:304-310), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto, et al., 1980, Cell 22:787-797), the herpes simplex thymidine kinase promoter (Wagner et al., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445), the regulatory sequences of the metallothionein gene (Brinster et al., 1982, Nature 296:3942); prokaryotic vectors containing promoters such as the β-lactamase promoter (Villa-Kamaroff, et al., 1978, Proc. Natl. Acad. Sci. U.S.A. 75:3727-3731), or the tac promoter (DeBoer, et al., 1983, Proc. Natl. Acad. Sci. U.S.A. 80:21-25); see also “Useful proteins from recombinant bacteria” in Scientific American, 1980, 242:74-94; plant expression vectors comprising the nopaline synthetase promoter region (Herrera-Estrella et al., 1983, Nature 303:209-213) or the cauliflower mosaic virus 35S RNA promoter (Gardner, et al., 1981, Nucl. Acids Res. 9:2871), and the promoter of the photosynthetic enzyme ribulose biphosphate carboxylase (Herrera-Estrella et al., 1984, Nature 310:115-120); promoter elements from yeast or fungi such as the Gal 4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase) promoter, and/or the alkaline phosphatase promoter.

The vectors according to the invention are, for example, vectors of plasmid or viral origin. In a specific embodiment, a vector is used that comprises a promoter operably linked to a protein or peptide-encoding nucleic acid sequence contained within the disclosed polynucleotide sequences, one or more origins of replication, and, optionally, one or more selectable markers (e.g., an antibiotic resistance gene). Expression vectors comprise regulatory sequences that control gene expression, including gene expression in a desired host cell. Exemplary vectors for the expression of the polypeptides of the invention include the pET-type plasmid vectors (Promega) or pBAD plasmid vectors (Invitrogen) or those provided in the examples below. Furthermore, the vectors according to the invention are useful for transforming host cells so as to clone or express the polynucleotide sequences of the invention.

The invention also encompasses the host cells transformed by a vector according to the invention. These cells may be obtained by introducing into host cells a nucleotide sequence inserted into a vector as defined above, and then culturing the said cells under conditions allowing the replication and/or the expression of the polynucleotide sequences of the subject invention.

The host cell may be chosen from eukaryotic or prokaryotic systems, such as for example bacterial cells, (Gram negative or Gram positive), yeast cells (for example, Saccharomyces cereviseae or Pichia pastoris), animal cells (such as Chinese hamster ovary (CHO) cells), plant cells, and/or insect cells using baculovirus vectors. In some embodiments, the host cells for expression of the polypeptides include, and are not limited to, those taught in U.S. Pat. Nos. 6,319,691, 6,277,375, 5,643,570, or 5,565,335, each of which is incorporated by reference in its entirety, including all references cited within each respective patent.

Furthermore, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Expression from certain promoters can be elevated in the presence of certain inducers; thus, expression of the genetically engineered polypeptide may be controlled. Furthermore, different host cells have characteristic and specific mechanisms for the translational and post-translational processing and modification (e.g., glycosylation, phosphorylation) of proteins. Appropriate cell lines or host systems can be chosen to ensure the desired modification and processing of the foreign protein expressed. For example, expression in a bacterial system can be used to produce an unglycosylated core protein product. Expression in yeast will produce a glycosylated product. Expression in mammalian cells can be used to ensure “native” glycosylation of a heterologous protein. Furthermore, different vector/host expression systems may effect processing reactions to different extents.

The subject invention also concerns novel compositions that can be employed to elicit an immune response or a protective immune response. In this aspect of the invention, an amount of a composition comprising recombinant DNA or mRNA encoding an polynucleotide of the subject invention sufficient to elicit an immune response or protective immune response is administered to an individual. Signal sequences may be deleted from the nucleic acid encoding an antigen of interest and the individual may be monitored for the induction of an immune response according to methods known in the art. A “protective immune response” or “therapeutic immune response” refers to a CTL (or CD8⁺ T cell) and/or an HTL (or CD4⁺ T cell) response to an antigen that, in some way, prevents or at least partially arrests disease symptoms, side effects or progression. The immune response may also include an antibody response that has been facilitated by the stimulation of helper T cells.

In another embodiment, the subject invention further comprises the administration of polynucleotide vaccines in conjunction with a polypeptide antigen, or composition thereof, of the invention. In a preferred embodiment, the antigen is the polypeptide that is encoded by the polynucleotide administered as the polynucleotide vaccine. As a particularly preferred embodiment, the polypeptide antigen is administered as a booster subsequent to the initial administration of the polynucleotide vaccine.

A further embodiment of the subject invention provides for the induction of an immune response to the novel Plasmodium falciparum antigens disclosed herein (see, for example, the antigens and peptides set forth in the Tables and Sequence Listing attached hereto) using a “prime-boost” vaccination regimen known to those skilled in the art. In this aspect of the invention, a DNA vaccine is administered to an individual in an amount sufficient to “prime” the immune response of the individual, provided that the DNA vaccine comprises nucleic acids encoding the antigens, multi-epitope constructs, and/or peptide antigens set forth herein. The immune response of the individual is then “boosted” via the administration of: 1) one or a combination of: a peptide, polypeptide, and/or full length polypeptide antigen (e.g., SEQ ID NOs: 1-27) of the subject invention (optionally in conjunction with a immunostimulatory molecule and/or an adjuvant); or 2) a viral vector that contains nucleic acid encoding one, or more, of the same or, optionally, different, antigens, multi-epitope constructs, and/or peptide antigens set forth in the Tables or Sequence Listing of the subject application. In some alternative embodiments of the invention, a gene encoding an immunostimulatory molecule may be incorporated into the viral vector used to “boost the immune response of the individual. Exemplary immunostimulatory molecules include, and are not limited to, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-15, Il-16, Il-18, IL-23, IL-24, erythropoietin, G-CSF, M-CSF, platelet derived growth factor (PDGF), MSF, FLT-3 ligand, EGF, fibroblast growth factor (FGF; e.g., aFGF (FGF-1), bFGF (FGF-2), FGF-3, FGF-4, FGF-5, FGF-6, or FGF-7), insulin-like growth factors (e.g., IGF-1, IGF-2); vascular endothelial growth factor (VEGF); interferons (e.g., IFN-γ, IFN-α, IFN-β); leukemia inhibitory factor (LIF); ciliary neurotrophic factor (CNTF); oncostatin M; stem cell factor (SCF); transforming growth factors (e.g., TGF-α, TGF-β1, TGF-β1, TGF-β1), or chemokines (such as, but not limited to, BCA-1/BLC-1, BRAK/Kec, CXCL16, CXCR3, ENA-78/LIX, Eotaxin-1, Eotaxin-2/MPIF-2, Exodus-2/SLC, Fractalkine/Neurotactin, GROalpha/MGSA, HCC-1, I-TAC, Lymphotactin/ATAC/SCM, MCP-1/MCAF, MCP-3, MCP-4, MDC/STCP-1, ABCD-1, MIP-1α, MIP-1β, MIP-2α/GROβ, MIP-3α/Exodus/LARC, MIP-3β/Exodus-3/ELC, MIP4/PARC/DC-CK1, PFA, RANTES, SDF1α, TARC, or TECK). Genes encoding these immunostimulatory molecules are known to those skilled in the art and coding sequences may be obtained from a variety of sources, including various patents databases, publicly available databases (such as the nucleic acid and protein databases found at the National Library of Medicine or the European Molecular Biology Laboratory), the scientific literature, or scientific literature cited in catalogs produced by companies such as Genzyme, Inc., R&D Systems, Inc, or InvivoGen, Inc. [see, for example, the 1995 Cytokine Research Products catalog, Genzyme Diagnostics, Genzyme Corporation, Cambridge Mass.; 2002 or 1995 Catalog of R&D Systems, Inc (Minneapolis, Minn.); or 2002 Catalog of InvivoGen, Inc (San Diego, Calif.) each of which is incorporated by reference in its entirety, including all references cited therein].

Methods of introducing DNA vaccines into individuals are well-known to the skilled artisan. For example, DNA can be injected into skeletal muscle or other somatic tissues (e.g., intramuscular injection). Cationic liposomes or biolistic devices, such as a gene gun, can be used to deliver DNA vaccines. Alternatively, iontophoresis and other means for transdermal transmission can be used for the introduction of DNA vaccines into an individual.

Viral vectors for use in the subject invention can have a portion of the viral genome deleted to introduce new genes without destroying infectivity of the virus. The viral vector of the present invention is, typically, a non-pathogenic virus. At the option of the practitioner, the viral vector can be selected so as to infect a specific cell type, such as professional antigen presenting cells (e.g., macrophage or dendritic cells). Alternatively, a viral vector can be selected that is able to infect any cell in the individual. Exemplary viral vectors suitable for use in the present invention include, but are not limited to poxvirus such as vaccinia virus, avipox virus, fowlpox virus, a highly attenuated vaccinia virus (such as Ankara or MVA [Modified Vaccinia Ankara]), retrovirus, adenovirus, baculovirus and the like. In a preferred embodiment, the viral vector is Ankara or MVA.

General strategies for construction of vaccinia virus expression vectors are known in the art (see, for example, Smith and Moss Bio Techniques Nov/Dec, 306-312, 1984; U.S. Pat. No. 4,738,846 (hereby incorporated by reference in its entirety). Sutter and Moss (Proc. Nat'l. Acad. Sci U.S.A. 89:10847-10851, 1992) and Sutter et al. (Vaccine, 12(11):103240, 1994) disclose the construction and use as a vector, a non-replicating recombinant Ankara virus (MVA) which can be used as a viral vector in the present invention. Other versions of the Modified Vaccinia Ankara strain can also be used in the practice of the subject invention (such as the MVA-BN strain produced by Bavarian Nordic S/A (Copenhagen, Denmark).

Compositions comprising the subject polynucleotides can include appropriate nucleic acid vaccine vectors (plasmids), which are commercially available (e.g., Vical, San Diego, Calif.) or other nucleic acid vectors (plasmids), which are also commercially available (e.g., Valenti, Burlingame, Calif.). Alternatively, compositions comprising viral vectors and polynucleotides according to the subject invention are provided by the subject invention. In addition, the compositions can include a pharmaceutically acceptable carrier, e.g., saline. The pharmaceutically acceptable carriers are well known in the art and also are commercially available. For example, such acceptable carriers are described in E. W. Martin's Remington's Pharmaceutical Science, Mack Publishing Company, Easton, Pa.

The subject invention also provides one or more isolated polypeptides comprising:

a) a polypeptide encoded by a polynucleotide sequence according to embodiment A(a) (set forth above);

b) a variant polypeptide encoded by a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide according to embodiment A(a) (as set forth above);

c) a fragment of a polypeptide or a variant polypeptide, wherein said fragment or variant has substantially the same serologic reactivity or substantially the same T-cell reactivity as the native polypeptide (e.g., those polypeptides set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 and Table 2, 3, 4, 5 or 6);

d) a polypeptide sequence provided in Table 2, 3, 4, 5 or 6 or selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27;

e) a variant polypeptide having at least about 20% to 99.99% identity to a polypeptide provided in Table 2, 3, 4, 5 or 6 or selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27;

f) a polypeptide (epitope) set forth in Table 2, 3, 4, 5 or 6; or

g) a multi-epitope construct: 1) comprising at least one epitope set forth in Table 2, 3, 4, 5 or 6; 2) comprising a polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27 and at least one epitope set forth in Tables 2, 3, 4, 5 or 6; or 3) comprising and at least one epitope set forth in Tables 2, 3, 4, 5 or 6 and one or more polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27.

The term “peptide” may be used interchangeably with “oligopeptide” or “polypeptide” or “epitope” in the present specification to designate a series of residues, typically L-amino acids, connected one to the other, typically by peptide bonds between the α-amino and carboxyl groups of adjacent amino acids. The preferred CTL (or CD8⁺ T cell)-inducing peptides of the invention are 13 residues or less in length and usually consist of between about 8 and about 11 residues (e.g., 8, 9, 10 or 11 residues), preferably 9 or 10 residues. The preferred HTL (or CD4⁺ T cell)-inducing peptides are less than about 50 residues in length and usually consist of between about 6 and about 30 residues, more usually between about 12 and 25 (e.g., 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25), and often between about 15 and 20 residues (e.g., 15, 16, 17, 18, 19 or 20).

According to the subject invention, a “fragment” is a polypeptide of at least 3 consecutive, preferably 4 consecutive, and even more preferably 5 consecutive amino acids. In some embodiments, the polypeptide fragments are reactive with antibodies found in the serum of an individual. In other embodiments, a fragment is an “epitope” as described supra. In the context of the instant invention, the terms polypeptide, peptide and protein can be used interchangeably; however, it should be understood that the invention does not relate to the polypeptides in natural form, that is to say that they are not in their natural environment but that the polypeptides may have been isolated or obtained by purification from natural sources, obtained from host cells prepared by genetic manipulation (e.g., the polypeptides, or fragments thereof, are recombinantly produced by host cells, or by chemical synthesis). Polypeptides according to the instant invention may also contain non-natural amino acids, as will be described below.

A “variant” or “modified” polypeptide (or polypeptide variant) is to be understood to designate polypeptides exhibiting, in relation to the natural polypeptide, certain modifications. These modifications can include a deletion, addition, or substitution of at least one amino acid, a truncation, an extension, a chimeric fusion, a mutation, or polypeptides exhibiting post-translational modifications. Among the homologous polypeptides, those whose amino acid sequences exhibit between at least (or at least about) 20.00% to 99.99% (inclusive) identity to the full length, native, or naturally occurring polypeptide are another aspect of the invention. The aforementioned range of percent identity is to be taken as including, and providing written description and support for, any fractional percentage, in intervals of 0.01%, between 20.00% and, up to, including 99.99%. These percentages are purely statistical and differences between two polypeptide sequences can be distributed randomly and over the entire sequence length.

Variant peptides (epitopes) can also be created by altering the presence or absence of particular residues in these primary anchor positions. Such analogs are used to modulate the binding affinity of a peptide comprising a particular motif or supermotif. The term “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif (e.g., 8, 9, 10, 11, 12 or 13 aa) and from about 6 to about 25 amino acids for a class II HLA motif (e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids), which is recognized by a particular HLA molecule. Peptide motifs are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues. Optionally, variant peptides or polypeptides can also comprise one or more heterologous polypeptide sequences (e.g., tags that facilitate purification of the polypeptides of the invention (see, for example, U.S. Pat. No. 6,342,362, hereby incorporated by reference in its entirety; Altendorf et al. [1999-WWW, 2000] “Structure and Function of the F₀ Complex of the ATP Synthase from Escherichia Coli,” J. of Experimental Biology 203:19-28, The Co. of Biologists, Ltd., G. B.; Baneyx [1999] “Recombinant Protein Expression in Escherichia coli,” Biotechnology 10:411-21, Elsevier Science Ltd.; Eihauer et al. [2001] “The FLAG™ Peptide, a Versatile Fusion Tag for the Purification of Recombinant Proteins,” J. Biochem Biophys Methods 49:455-65; Jones et al. [1995] J. Chromatography 707:3-22; Jones et al. [1995] “Current Trends in Molecular Recognition and Bioseparation,” J. of Chromatography A. 707:3-22, Elsevier Science B. V.; Margolin [2000] “Green Fluorescent Protein as a Reporter for Macromolecular Localization in Bacterial Cells,” Methods 20:62-72, Academic Press; Puig et al. [2001] “The Tandem Affinity Purification (TAP) Method: A General Procedure of Protein Complex Purification,” Methods 24:218-29, Academic Press; Sassenfeld [1990] “Engineering Proteins for Purification,” TibTech 8:88-93; Sheibani [1999] “Prokaryotic Gene Fusion Expression Systems and Their Use in Structural and Functional Studies of Proteins,” Prep. Biochem. & Biotechnol. 29(1):77-90, Marcel Dekker, Inc.; Skerra et al [1999] “Applications of a Peptide Ligand for Streptavidin: the Strep-tag”, Biomolecular Engineering 16:79-86, Elsevier Science, B. V.; Smith [1998] “Cookbook for Eukaryotic Protein Expression: Yeast, Insect, and Plant Expression Systems,” The Scientist 12(22):20; Smyth et al [2000] “Eukaryotic Expression and Purification of Recombinant Extracellular Matrix Proteins Carrying the Strep II Tag”, Methods in Molecular Biology, 139:49-57; Unger [1997] “Show Me the Money: Prokaryotic Expression Vectors and Purification Systems,” The Scientist 11(17):20, each of which is hereby incorporated by reference in their entireties), or commercially available tags from vendors such as such as STRATAGENE (La Jolla, Calif.), NOVAGEN (Madison, Wis.), QIAGEN, Inc., (Valencia, Calif.), or InVitrogen (San Diego, Calif.).

Variant polypeptides can, alternatively, have 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent identity with the polypeptide sequences of the instant invention. In a preferred embodiment, a variant or modified polypeptide exhibits approximately 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a natural polypeptic of the invention. Typically, the percent identity is calculated with reference to the full length, native, and/or naturally occurring polypeptide (e.g., those polypeptides set forth in SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27).

The nomenclature used to describe peptide compounds follows the conventional practice wherein the amino group is presented to the left (the N-terminus) and the carboxyl group to the right (the C-terminus) of each amino acid residue. When amino acid residue positions are referred to in an epitope, they are numbered in an amino to carboxyl direction with position one being the position closest to the amino terminal end of the epitope, or the peptide or protein of which it may be a part. In the formulae representing selected specific embodiments of the present invention, the amino- and carboxyl-terminal groups, although not specifically shown, are in the form they would assume at physiologic pH values, unless otherwise specified. In the amino acid structure formulae, each residue is generally represented by standard three-letter or single-letter designations (e.g., as set forth infra). By way of example, amino acid substitutions can be carried out without resulting in a substantial modification of the biological activity of the corresponding modified polypeptides; for example, the replacement of leucine with valine or isoleucine, of aspartic acid with glutamic acid, of glutamine with asparagine, of arginine with lysine, and the like, the reverse substitutions can be performed without substantial modification of the biological activity of the polypeptides.

The L-form of an amino acid residue is represented by a capital single letter or a capital first letter of a three-letter symbol, and the D-form, for those amino acids having D-forms, is represented by a lower case single letter or a lower case three letter symbol. Glycine has no asymmetric carbon atom and is simply referred to as “Gly” or G. Symbols for the amino acids are as follows: (Single Letter Symbol; Three Letter Symbol Amino Acid) A; Ala; Alanine: C; Cys; Cysteine: D; Asp; Aspartic Acid: E; Glu; Glutamic Acid: F; Phe; Phenylalanine: G; Gly; Glycine: H; His; Histidine: I; Ile; Isoleucine: K; Lys; Lysine: L; Leu; Leucine: M; Met; Methionine: N; Asn; Asparagine: P; Pro; Proline: Q; Gln; Glutamine: R; Arg; Arginine: S; Ser; Serine: T; Thr; Threonine: V; Val; Valine: W; Trp; Tryptophan: Y; Tyr; Tyrosine.

Amino acid “chemical characteristics” are defined as: Aromatic (F, W, Y); Aliphatic-hydrophobic (L, I, V, M); Small polar (S, T, C); Large polar (Q, N); Acidic (D, E); Basic (R, H, K); Non-polar: Proline; Alanine; and Glycine.

In order to extend the life of the polypeptides according to the invention, it may be advantageous to use non-natural amino acids, for example in the D-form, or alternatively amino acid analogs, for example sulfur-containing forms of amino acids in the production of “variant polypeptides”. Alternative means for increasing the life of polypeptides can also be used in the practice of the instant invention. For example, polypeptides of the invention, and fragments thereof, can be recombinantly modified to include elements that increase the plasma, or serum half-life of the polypeptides of the invention. These elements include, and are not limited to, antibody constant regions (see for example, U.S. Pat. No. 5,565,335, hereby incorporated by reference in its entirety, including all references cited therein), or other elements such as those disclosed in U.S. Pat. Nos. 6,319,691, 6,277,375, or 5,643,570, each of which is incorporated by reference in its entirety, including all references cited within each respective patent. Alternatively, the polynucleotides and genes of the instant invention can be recombinantly fused to elements, well known to the skilled artisan, that are useful in the preparation of immunogenic constructs for the purposes of vaccine formulation.

The subject invention also provides biologically active fragments (epitopes) of a polypeptide according to the invention and includes those peptides capable of eliciting an immune response directed against P. falciparum, said immune response providing components (B-cells, antibodies, and/or or components of the cellular immune response (e.g., helper, cytotoxic, and/or suppressor T-cells)) reactive with the biologically active fragment of a polypeptide; the intact, full length, unmodified polypeptide disclosed herein; or both the biologically active fragment of a polypeptide and the intact, full length, unmodified polypeptides disclosed herein.

Fragments, as described herein, can be obtained by cleaving the polypeptides of the invention with a proteolytic enzyme (such as trypsin, chymotrypsin, or collagenase) or with a chemical reagent, such as cyanogen bromide (CNBr). Alternatively, polypeptide fragments can be generated in a highly acidic environment, for example at pH 2.5. Such polypeptide fragments may be equally well prepared by chemical synthesis or using hosts transformed with an expression vector according to the invention. The transformed host cells contain a nucleic acid, allowing the expression of these fragments, under the control of appropriate elements for regulation and/or expression of the polypeptide fragments.

In one embodiment, the subject invention provides methods for eliciting an immune response in an individual comprising the administration of compositions comprising polypeptides according to the subject invention to an individual in amounts sufficient to induce an immune response in the individual. In some embodiments, a “protective” or “therapeutic immune response” is induced in the individual. A “protective immune response” or “therapeutic immune response” refers to a CTL (or CD8⁺ T cell) and/or an HTL (or CD4⁺ T cell), and/or an antibody response to an antigen derived from an infectious agent or a tumor antigen, which in some way prevents or at least partially arrests disease symptoms, side effects or progression. The protective immune response may also include an antibody response that has been facilitated by the stimulation of helper T cells (or CD4⁺ T cells). Additional methods of inducing an immune response in an individual are taught in U.S. Pat. No. 6,419,931, hereby incorporated by reference in its entirety. The term CTL can be used interchangeably with CD8⁺ T-cell(s) and the term HTL can be used interchangeably with CD4⁺ T-cell(s) throughout the subject application.

The term “individual” includes mammals which include, and are not limited to, apes, chimpanzees, orangutans, humans, monkeys or domesticated animals (pets) such as dogs, cats, guinea pigs, hamsters, Vietnamese pot-bellied pigs, rabbits, ferrets, cows, horses, goats and sheep. In a preferred embodiment, the methods of inducing an immune response contemplated herein are practiced on humans.

Another embodiment of the subject invention provides methods of inducing an immune response in an individual comprising the administration of a composition comprising polypeptides encoded by the polynucleotides of the subject invention in amounts sufficient to induce an immune response. In some embodiments of the invention, the immune response provides protective immunity. The composition administered to the individual may, optionally, contain an adjuvant and may be delivered in any manner known in the art for the delivery of immunogen to a subject. Compositions may also be formulated in any carriers, including for example, pharmaceutically acceptable carriers such as those described in E. W. Martin's Remington's Pharmaceutical Science, Mack Publishing Company, Easton, Pa. In a preferred embodiment, compositions may be formulated in incomplete Freund's adjuvant.

In various embodiments, the subject invention provides for diagnostic assays based upon Western blot formats or standard immunoassays known to the skilled artisan. For example, antibody-based assays such as enzyme linked immunosorbent assays (ELISAs), radioimmunoassays (RIAs), lateral flow assays, immunochromatographic strip assays, automated flow assays, and assays utilizing antibody-containing biosensors may be employed for the detection of the polypeptides, and fragments thereof, provided by the subject invention. The assays and methods for conducting the assays are well-known in the art and the methods may test biological samples qualitatively (presence or absence of polypeptide) or quantitatively (comparison of a sample against a standard curve prepared using a polypeptide of the subject invention) for the presence of one or more polypeptide of the subject invention. Thus, the subject invention provides a method of detecting a P. falciparum polypeptide, or fragment thereof, comprising contacting a sample with an antibody that specifically binds to a polypeptide, or fragment thereof, comprising SEQ ID NOs: 1-26, or 27 and detecting the presence of an antibody-antigen complex.

The antibody-based assays can be considered to be of four types: direct binding assays, sandwich assays, competition assays, and displacement assays. In a direct binding assay, either the antibody or antigen is labeled, and there is a means of measuring the number of complexes formed. In a sandwich assay, the formation of a complex of at least three components (e.g., antibody-antigen-antibody) is measured. In a competition assay, labeled antigen and unlabelled antigen compete for binding to the antibody, and either the bound or the free component is measured. In a displacement assay, the labeled antigen is pre-bound to the antibody, and a change in signal is measured as the unlabelled antigen displaces the bound, labeled antigen from the receptor.

Lateral flow assays can be conducted according to the teachings of U.S. Pat. No. 5,712,170 and the references cited therein. U.S. Pat. No. 5,712,170 and the references cited therein are hereby incorporated by reference in their entireties. Displacement assays and flow immunosensors useful for carrying out displacement assays are described in: (1) Kusterbeck et al., “Antibody-Based Biosensor for Continuous Monitoring”, in Biosensor Technology, R. P. Buck et al., eds., Marcel Dekker, N.Y. pp. 345-350 (1990); Kusterbeck et al., “A Continuous Flow Immunoassay for Rapid and Sensitive Detection of Small Molecules”, Journal of Immunological Methods, vol. 135, pp. 191-197 (1990); Ligler et al., “Drug Detection Using the Flow Immunosensor”, in Biosensor Design and Application, J. Findley et al., eds., American Chemical Society Press, pp. 73-80 (1992); and Ogert et al., “Detection of Cocaine Using the Flow Immunosensor”, Analytical Letters, vol. 25, pp. 1999-2019 (1992), all of which are incorporated herein by reference in their entireties. Displacement assays and flow immunosensors are also described in U.S. Pat. No. 5,183,740, which is also incorporated herein by reference in its entirety. The displacement immunoassay, unlike most of the competitive immunoassays used to detect small molecules, can generate a positive signal with increasing antigen concentration. One aspect of the invention allows for the exclusion of Western blots as a diagnostic assay, particularly where the Western blot is a screen of whole cell lysates of P. falciparum, or related organisms, against immune serum of infected individuals. In another aspect of the invention, peptide, or polypeptide, based diagnostic assays utilize P. falciparum peptides or polypeptides that have been produce either by chemical peptide synthesis or by recombinant methodologies that utilize non-plasmodium host cells for the production of peptides or polypeptides.

Another aspect of the invention provides for the use of peptides, polypeptides, and multi-epitope constructs in assays such as those taught in U.S. Pat. No. 5,635,363, which is hereby incorporated by reference in its entirety. Briefly, peptides, polypeptides, and multi-epitope constructs of the subject invention can be used to form stable multimeric complexes that comprise prepared major histocompatibility complex (MHC) protein subunits having a substantially homogeneous bound peptide population. The multimeric MHC-antigen complex forms a stable structure with T cells recognizing the complex through their antigen receptor, thereby allowing for the labeling, identification and separation of specific T cells. The multimeric binding complex has the formula (α-β-P)_(n), where n≧2, usually n≧4, and usually n≦10; α is an α chain of a class I or class II MHC protein. β is a β chain, (the β chain of a class II MHC protein or β₂ microglobulin for a MHC class I protein; and P is a peptide antigen. The multimeric complex stably binds through non-covalent interactions to a T cell receptor having the appropriate antigenic specificity. The MHC proteins may be from any individual. Of particular interest are the human HLA proteins. Included in the HLA proteins are the class II subunits HLA-DPα, HLA-DPβ, HLA-DQα, HLA-DQβ, HLA-DRα and HLA-DRβ, and the class I proteins HLA-A, HLA-B, HLA-C, and β₂-microglobulin. In a preferred embodiment, the MHC protein subunits are a soluble form of the normally membrane-bound protein. The soluble form is derived from the native form by deletion of the transmembrane domain. Conveniently, the protein is truncated, removing both the cytoplasmic and transmembrane domains. The protein may be truncated by proteolytic cleavage, or by expressing a genetically engineered truncated form. For class I proteins, the soluble form will include the α1, α2 and α3 domain. Not more than about 10, usually not more than about 5, preferably none of the amino acids of the transmembrane domain will be included. The deletion may extend as much as about 10 amino acids into the α3 domain, preferably none of the amino acids of the α3 domain will be deleted. The deletion will be such that it does not interfere with the ability of the α3 domain to fold into a disulfide bonded structure. The class I β chain, β₂-microglobulin, lacks a transmembrane domain in its native form, and need not be truncated. Generally, no Class II subunits will be used in conjunction with Class I subunits. Soluble class II subunits will include the α1 and α2 domains for the a subunit, and the β1 and β2 domains for the β subunit. Not more than about 10, usually not more than about 5, preferably none of the amino acids of the transmembrane domain will be included. The deletion may extend as much as about 10 amino acids into the α2 or β2 domain, preferably none of the amino acids of the β2 or β2 domain will be deleted. The deletion will be such that it does not interfere with the ability of the α2 or β2 domain to fold into a disulfide bonded structure.

The monomeric complex (α-β-P) (monomer) is multimerized. The resulting multimer will be stable over long periods of time. Usually not more than about 10% of the multimer will be dissociated after storage at 4° C. for about one day, more usually after about one week. Preferably, the multimer will be formed by binding the monomers to a multivalent entity through specific attachment sites on the α or β subunit, as described below in detail. The multimer may also be formed by chemical cross-linking of the monomers. A number of reagents capable of cross-linking proteins are known in the art, illustrative entities include: azidobenzoyl hydrazide, N-[4-(p-azidosalicylamino)butyl]-3′-[2′-pyridyldithio]propionamide), bis-sulfosuccinimidyl suberate, dimethyladipimidate, disuccinimidyltartrate, N-.gamma.-maleimidobutyryloxysuccinimide ester, N-hydroxy sulfosuccinimidyl-4-azidobenzoate, N-succinimidyl [4-azidophenyl]-1,3′-dithiopropionate, N-succinimidyl [4-iodoacetyl]aminobenzoate, glutaraldehyde, formaldehyde and succinimidyl 4-[N-maleimidomethyl]cyclohexane-1-carboxylate.

The attachment site for binding to a multivalent entity may be naturally occurring, or may be introduced through genetic engineering. The site will be a specific binding pair member or one that is modified to provide a specific binding pair member, where the complementary pair has a multiplicity of specific binding sites. Binding to the complementary binding member can be a chemical reaction, epitope-receptor binding or hapten-receptor binding where a hapten is linked to the subunit chain. In a preferred embodiment, one of the subunits is fused to an amino acid sequence providing a recognition site for a modifying enzyme. The recognition sequence will usually be fused proximal to the carboxy terminus of one of the subunit to avoid potential hindrance at the antigenic peptide binding site. Conveniently, an expression cassette will include the sequence encoding the recognition site.

Modifying enzymes of interest include BirA, various glycosylases, farnesyl protein transferase, protein kinases and the like. The subunit may be reacted with the modifying enzyme at any convenient time, usually after formation of the monomer. The group introduced by the modifying enzyme, e.g. biotin, sugar, phosphate, farnesyl, etc. provides a complementary binding pair member, or a unique site for further modification, such as chemical cross-linking, biotinylation, etc. that will provide a complementary binding pair member. An alternative strategy is to introduce an unpaired cysteine residue to the subunit, thereby introducing a unique and chemically reactive site for binding. The attachment site may also be a naturally occurring or introduced epitope, where the multivalent binding partner will be an antibody, e.g. IgG, IgM, etc. Any modification will be at a site, e.g. C-terminal proximal, that will not interfere with binding.

Exemplary of multimer formation is the introduction of the recognition sequence for the enzyme BirA, which catalyzes biotinylation of the protein substrate. The monomer with a biotinylated subunit is then bound to a multivalent binding partner, e.g. streptavidin or avidin, to which biotin binds with extremely high affinity. Streptavidin has a valency of 4, providing a multimer of (α-β-P)₄.

The multivalent binding partner may be free in solution, or may be attached to an insoluble support. Examples of suitable insoluble supports include beads, e.g. magnetic beads, membranes and microtiter plates. These are typically made of glass, plastic (e.g. polystyrene), polysaccharides, nylon or nitrocellulose. Attachment to an insoluble support is useful when the binding complex is to be used for separation of T cells.

Frequently, the multimeric complex will be labeled, so as to be directly detectable, or will be used in conjunction with secondary labeled immunoreagents which will specifically bind the complex. In general the label will have a light detectable characteristic. Preferred labels are fluorophors, such as fluorescein isothiocyanate (FITC), rhodamine, Texas Red, phycoerythrin and allophycocyanin. Other labels of interest may include dyes, enzymes, chemiluminescers, particles, radioisotopes, or other directly or indirectly detectable agent. Conveniently, the multivalent binding partner will have the labeling group. Alternatively, a second stage label may be used, e.g. labeled antibody directed to one of the peptide constituents, and the like.

The binding complex will be used to detect and/or separate antigen specific T cells. The T cells may be from any source, usually having the same species of origin as the MHC heterodimer. The T cells may be from an in vitro culture, or a physiologic sample. For the most part, the physiologic samples employed will be blood or lymph, but samples may also involve other sources oft cells, particularly where T cells may be invasive. Thus other sites of interest are tissues, or associated fluids, as in the brain, lymph node, neoplasms, spleen, liver, kidney, pancreas, tonsil, thymus, joints, synovia, and the like. The sample may be used as obtained or may be subject to modification, as in the case of dilution, concentration, or the like. Prior treatments may involve removal of cells by various techniques, including centrifugation, using Ficoll-Hypaque, panning, affinity separation, using antibodies specific for one or more markers present as surface membrane proteins on the surface of cells, or any other technique that provides enrichment of the set or subset of cells of interest.

The binding complex is added to a suspension comprising T cells of interest, and incubated at about 4° C. for a period of time sufficient to bind the available cell surface receptor. The incubation will usually be at least about 5 minutes and usually less than about 30 minutes. It is desirable to have a sufficient concentration of labeling reagent in the reaction mixture, so that labeling reaction is not limited by lack of labeling reagent. The appropriate concentration is determined by titration. The medium in which the cells are labeled will be any suitable medium as known in the art. If live cells are desired a medium will be chosen that maintains the viability of the cells. A preferred medium is phosphate buffered saline containing from 0.1 to 0.5% BSA. Various media are commercially available and may be used according to the nature of the cells, including Dulbecco's Modified Eagle Medium (dMEM), Hank's Basic Salt Solution (HBSS), Dulbecco's phosphate buffered saline (dPBS), RPMI, Iscove's medium, PBS with 5 mM EDTA, etc., frequently supplemented with fetal calf serum, BSA, HSA, etc.

Where a second stage labeling reagent is used, the cell suspension may be washed and resuspended in medium as described above prior to incubation with the second stage reagent. Alternatively, the second stage reagent may be added directly into the reaction mix.

A number of methods for detection and quantitation of labeled cells are known in the art. Flow cytometry is a convenient means of enumerating cells that are a small percent of the total population. Fluorescent microscopy may also be used. Various immunoassays, e.g. ELISA, RIA, etc. may used to quantitate the number of cells present after binding to an insoluble support.

Flow cyometry may also be used for the separation of a labeled subset of T cells from a complex mixture of cells. The cells may be collected in any appropriate medium which maintains the viability of the cells, usually having a cushion of serum at the bottom of the collection tube. Various media are commercially available as described above. The cells may then be used as appropriate.

Alternative means of separation utilize the binding complex bound directly or indirectly to an insoluble support, e.g. column, microtiter plate, magnetic beads, etc. The cell sample is added to the binding complex. The complex may be bound to the support by any convenient means. After incubation, the insoluble support is washed to remove non-bound components. From one to six washes may be employed, with sufficient volume to thoroughly wash non-specifically bound cells present in the sample. The desired cells are then eluted from the binding complex. In particular the use of magnetic particles to separate cell subsets from complex mixtures is described in Miltenyi et al. (1990) Cytometry 11:231-238.

Detecting and/or quantitating specific T cells in a sample or fraction thereof may be accomplished by a variety of specific assays. In general, the assay will measure the binding between a patient sample, usually blood derived, generally in the form of plasma or serum and the subject multimeric binding complexes. The patient sample may be used directly, orb diluted as appropriate, usually about 1:10 and usually not more than about 1:10,000. Assays may be performed in any physiological buffer, e.g. PBS, normal saline, HBSS, dPBS, etc.

A sandwich assay is performed by first attaching the multimeric binding complex to an insoluble surface or support. The multimeric binding complex may be bound to the surface by any convenient means, depending upon the nature of the surface, either directly or through specific antibodies. The particular manner of binding is not crucial so long as it is compatible with the reagents and overall methods of the invention. They may be bound to the plates covalently or non-covalently, preferably non-covalently.

The insoluble supports may be any compositions to which the multimeric binding complex can be bound, which is readily separated from soluble material, and which is otherwise compatible with the overall method of measuring T cells. The surface of such supports may be solid or porous and of any convenient shape. Examples of suitable insoluble supports to which the receptor is bound include beads, e.g. magnetic beads, membranes and microtiter plates. These are typically made of glass, plastic (e.g. polystyrene), polysaccharides, nylon or nitrocellulose. Microtiter plates are especially convenient because a large number of assays can be carried out simultaneously, using small amounts of reagents and samples.

Before adding patient samples or fractions thereof, the non-specific binding sites on the insoluble support i.e. those not occupied by the multimeric binding complex, are generally blocked. Preferred blocking agents include non-interfering proteins such as bovine serum albumin, casein, gelatin, and the like. Samples, fractions or aliquots thereof are then added to separately assayable supports (for example, separate wells of a microtiter plate) containing support-bound multimeric binding complex.

Generally from about 0.001 to 1 ml of sample, diluted or otherwise, is sufficient, usually about 0.01 ml sufficing. Preferably, each sample and standard will be added to multiple wells so that mean values can be obtained for each. The incubation time should be sufficient for T cells to bind the insoluble binding complex. Generally, from about 0.1 to 3 hr is sufficient, usually 1 hr sufficing.

After incubation, the insoluble support is generally washed of non-bound components. Generally, a dilute-physiologic buffer at-an appropriate pH, generally 7-8, is used as a wash medium. From one to six washes may be employed, with sufficient volume to thoroughly wash non-specifically bound T cells present in the sample.

After washing, a solution containing specific second receptor is applied. The receptor may be any compound that binds patient T cells with sufficient specificity such that they can be distinguished from other components present. In a preferred embodiment, second receptors are antibodies specific for common T cell antigens, either monoclonal or polyclonal sera, e.g. anti-thy-1, anti-CD45, etc.

T cell specific antibodies may be labeled to facilitate direct or indirect quantification of binding. Examples of labels that permit direct measurement include radiolabels, such as ³H or ¹²⁵I, fluorescers, dyes, beads, chemiluminescers, colloidal particles, and the like. Examples of labels which permit indirect measurement of binding include enzymes where the substrate may provide for a colored or fluorescent product. Examples of suitable enzymes for use in conjugates include horseradish peroxidase, alkaline phosphatase, malate dehydrogenase and the like. Where not commercially available, such antibody-enzyme conjugates are readily produced by techniques known to those skilled in the art.

Alternatively, the second receptor may be unlabeled. In this case, a labeled second receptor-specific compound is employed which binds to the bound second receptor. Such a second receptor-specific compound can be labelled in any of the above manners. It is possible to select such compounds such that multiple compounds bind each molecule of bound second receptor. Examples of second receptor/second receptor-specific molecule pairs include antibody/anti-antibody and avidin (or streptavidin)/biotin. Since the resultant signal is thus amplified, this technique may be advantageous where only a small number oft cells are present. An example is the use of a labeled antibody specific to the second receptor. More specifically, where the second receptor is a rabbit anti-allotypic antibody, an antibody directed against the constant region of rabbit antibodies provides a suitable second receptor specific molecule. The anti-immunoglobulin will usually come from any source other than human, such as ovine, rodentia, particularly mouse, or bovine.

The volume, composition and concentration of T cell specific receptor solution provides for measurable binding to the T cells already bound to the insoluble substrate. Generally, the same volume as that of the sample is used: from about 0.001 to 1 ml is sufficient, usually about 0.1 ml sufficing. When antibody ligands are used, the concentration generally will be about 0.1 to 50 μg/ml, preferably about 1 μg/ml. The solution containing the second receptor is generally buffered in the range of about pH 6.5-9.5. The solution may also contain an innocuous protein as previously described. The incubation time should be sufficient for the labeled ligand to bind available molecules. Generally, from about 0.1 to 3 hr is sufficient, usually 1 hr sufficing.

After the second receptor or second receptor-conjugate has bound, the insoluble support is generally again washed free of non-specifically bound second receptor, essentially as described for prior washes. After non-specifically bound material has been cleared, the signal produced by the bound conjugate is detected by conventional means. Where an enzyme conjugate is used, an appropriate enzyme substrate is provided so a detectable product is formed. More specifically, where a peroxidase is the selected enzyme conjugate, a preferred substrate combination is H₂O₂ and O-phenylenediamine which yields a colored product under appropriate reaction conditions. Appropriate substrates for other enzyme conjugates such as those disclosed above are known to those skilled in the art. Suitable reaction conditions as well as means for detecting the various useful conjugates or their products are also known to those skilled in the art. For the product of the substrate O-phenylenediamine for example, light absorbance at 490-495 nm is conveniently measured with a spectrophotometer.

Generally the number of bound T cells detected will be compared to control samples from samples having a different MHC context, e.g. T cells from an animal that does not express the MHC molecule used to make the binding complex.

An alternative protocol is to provide anti-T cell reagent, e.g. anti-thy-1, anti-CD45, etc. bound to the insoluble surface. After adding the sample and washing away non-specifically bound T cells, one or a combination of the subject binding complexes are added, where the binding complexes are labeled so as not to interfere with the binding to T cells.

It is particularly convenient in a clinical setting to perform the assays in a -self-contained apparatus. A number of such methods are known in the art. The apparatus will generally employ a continuous flow-path of a suitable filter or membrane, having at least three regions, a fluid transport region, a sample region, and a measuring region. The sample region is prevented from fluid transfer contact with the other portions of the flow path prior to receiving the sample. After the sample region receives the sample, it is brought into fluid transfer relationship with the other regions, and the fluid transfer region contacted with fluid to permit a reagent solution to pass through the sample region and into the measuring region. The measuring region may have bound to it the multimeric binding complex, with a conjugate of an enzyme with T cell specific antibody employed as a reagent, generally added to the sample before application. Alternatively, the binding complex may be conjugated to an enzyme, with T cell specific antibody bound to the measurement region.

Detection of T cells is of interest in connection with a variety of conditions associated with T cell activation. Such conditions include autoimmune diseases, e.g. multiple sclerosis, myasthenia gravis, rheumatoid arthritis, type 1 diabetes, graft vs. host disease, Grave's disease, etc.; various forms of cancer, e.g. carcinomas, melanomas, sarcomas, lymphomas and leukemias. Various infectious diseases such as those caused by viruses, e.g. HIV-1, hepatitis, herpesviruses, enteric viruses, respiratory viruses, rhabdovirus, rubeola, poxvirus, paramyxovirus, morbillivirus, etc. are of interest. Infectious agents of interest also include bacteria, such as Pneumococcus, Staphylococcus, Bacillus. Streptococcus, Meningococcus, Gonococcus, Eschericia, Klebsiella, Proteus, Pseudomonas, Salmonella, Shigella, Hemophilus, Yersinia, Listeria, Corynebacterium, Vibrio, Clostridia, Chlamydia, Mycobacterium, Helicobacter and Treponema; protozoan pathogens, and the like. T cell associated allergic responses may also be monitored, e.g. delayed type hypersensitivity or contact hypersensitivity involving T cells.

Of particular interest are conditions having an association with a specific peptide or MHC haplotype, where the subject binding complexes may be used to track the T cell response with respect to the haplotype and antigen. A large number of associations have been made in disease states that suggest that specific MHC haplotypes, or specific protein antigens are responsible for disease states.

Polypeptide fragments, including immunogenic fragments, for each of SEQ ID NOs: 1-27 can be any length from at least 5 consecutive amino acids to 1 amino acid less than a full length polypeptide of any given SEQ ID NO:. Thus, for SEQ ID NO: 1 (used here as a non-limiting example) the polypeptide fragment can contain any number of consecutive amino acids from 5 to 1903 (for example, 5, 6, 7, . . . , 1901, 1902, 1903). For the sake of brevity, the individual integers between 5 and 1903 have not been reproduced herein but are, in fact, specifically contemplated. In one embodiment, the immunogenic fragments of the invention induce immunity or protective immunity from disease.

The present invention also provides for the exclusion of any individual fragment (of any given SEQ ID NO:) specified by N-terminal to C-terminal positions, actual sequence, or of any fragment specified by size (in amino acid residues) as described above. In addition, any number of fragments specified by N-terminal and C-terminal positions, actual sequence, or by size (in amino acid residues) as described above may be excluded as individual species. Further, any number of fragments specified by N-terminal and C-terminal positions or by size (in amino acid residues) as described above may be combined to provide a polypeptide fragment. These types of fragments may, optionally, include polypeptide sequences such as linkers, described below.

Where a claim recites “a polypeptide comprising SEQ ID NO: X, or fragments or immunogenic fragments or epitopes of SEQ ID NO:X”, the language “fragments or immunogenic fragments or epitopes of SEQ ID NO:X” specifically excludes identical sub-sequences found within other longer naturally occurring prior art polypeptide or protein sequences that are not identical to sequence from which the claimed sequence was derived. This does not include instances where such sub-sequences are a part of a larger molecule specifically modified by the hand of man to enhance the immunogenicity of the fragments of the subject invention. Thus, fragments or immunogenic fragments or epitopes of SEQ ID NO:X specifically exclude, and are not to be considered anticipated, where the fragment is a sub-sequence of another naturally occurring non-malarial peptide, polypeptide, or protein isolated from a bacterial, viral, reptilian, insect, avian, or mammalian source and is identified in a search of protein sequence databases.

Fragments or immunogenic fragments or epitopes of the invention may further contain linkers that facilitate the attachment of the fragments to a carrier molecule for the stimulation of an immune response or diagnostic purposes. The linkers can also be used to attach fragments according to the invention to solid support matrices for use in affinity purification protocols. In this aspect of the invention, the linkers specifically exclude, and are not to be considered anticipated, where the fragment is a subsequence of another peptide, polypeptide, or protein as identified in a search of protein sequence databases as indicated in the preceding paragraph. In other words, the non-identical portions of the other peptide, polypeptide, of protein are not considered to be a “linker” in this aspect of the invention. Non-limiting examples of “linkers” suitable for the practice of the invention include chemical linkers (such as those sold by Pierce, Rockford, Ill.) and peptides that allow for the connection of the immunogenic fragment to a carrier molecule (see, for example, linkers disclosed in U.S. Pat. Nos. 6,121,424, 5,843,464, 5,750,352, and 5,990,275, hereby incorporated by reference in their entirety). In various embodiments, the linkers can be up to 50 amino acids in length, up to 40 amino acids in length, up to 30 amino acids in length, up to 20 amino acids in length, up to 10 amino acids in length, or up to 5 amino acids in length. Of course, the linker may be any pre-selected number of amino acids (up to 50 amino acids) in length.

In various embodiments, polypeptides suitable for use in various disclosed methods of the subject invention can be selected from the group consisting of: a) a polypeptide comprising a polypeptide sequence selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; b) a variant polypeptide having at least about 20% to 99.99% identity to a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; c) a fragment of a polypeptide or a variant polypeptide of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27, wherein said fragment or variant has substantially the same serologic reactivity or substantially the same T-cell reactivity as the native polypeptide; d) a multi-epitope construct; and e) combinations thereof.

Multi-Epitope Constructs

As indicated supra, the subject invention provides for “multi-epitope constructs”. A “multi-epitope construct” comprises: 1) nucleic acids that encode multiple polypeptide epitopes (of any length) that can bind to one or more molecules functioning in the immune system; or 2) polypeptides comprising multiple polypeptide epitopes that can bind to one or more molecules functioning in the immune system. “Multi-epitope constructs” can, optionally, contain “flanking” or “spacing” residues between each epitope. Some embodiments provide for “multi-epitope constructs” that comprise a series of the same epitope (termed “homopolymers”). Other embodiments provide for “multi-epitope constructs” that comprise a combination or series of different epitopes, optionally connected by “flanking” or “spacing” residues (termed “heteropolymers”). In some embodiments, “multi-epitope constructs” may exclude full-length polypeptides from which the epitopes are obtained (e.g., the polypeptides of SEQ ID NOs: 1-27). In certain preferred embodiments, the epitopes used in the formation of the multi-epitope construct are selected from those set forth in Table 2, Table 3, Table 4, Table 5, and/or Table 6 and any epitope set forth in these Tables 2-6 can be mixed and/or matched any other epitope set forth in any of the aforementioned Tables 2-6.

Multi-epitope constructs may be of “high affinity” or “intermediate affinity”. As used herein, “high affinity” with respect to HLA class I molecules is defined as binding with an IC₅₀, or KD value, of 50 nM or less; “intermediate affinity” with respect to HLA class I molecules is defined as binding with an IC₅₀ or KD value of between about 50 and about 500 nM. “High affinity” with respect to binding to HLA class II molecules is defined as binding with an IC₅₀ or KD value of 100 nM or less; “intermediate affinity” with respect to binding to HLA class II molecules is defined as binding with an IC₅₀ or KD value of between about 100 and about 1000 nM.

The multi-epitope constructs described herein preferably include five or more, ten or more, fifteen or more, twenty or more, or twenty-five or more epitopes. Other embodiments provide multi-epitope constructs that comprise at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 epitopes. All of the epitopes in a multi-epitope construct may be from one organism (e.g., the epitopes are obtained from P. falciparum), or the multi-epitope construct may include epitopes present in two or more different organisms (e.g., some epitopes from P. falciparum and some epitopes from another organism). Additionally, the same epitope may be present in a multi-epitope construct at more than one location in the construct. In some embodiments, novel epitopes of the subject invention may be linked to known epitopes of an organism (e.g., P. falciparum or another organism).

A “multi-epitope vaccine,” is a vaccine comprising multiple epitopes. A multi-epitope vaccine can induce an immune response and is administered to an individual in an amount sufficient to induce an immune response in the individual. In some embodiments, the immune response induced by the multi-epitope vaccine is a protective immune response against a given organism, pathogen, or pathologic condition (e.g., P. falciparum).

In certain embodiments, the epitopes of a multi-epitope construct or the polypeptides disclosed herein interact with an antigen binding site of an antibody molecule, a class I HLA, a T-cell receptor, and/or a class II HLA molecule. In certain preferred embodiments, the epitopes interact with an HLA molecule (e.g., class I or class II) or a T-cell receptor. In an even more preferred embodiment, the epitope interacts with both an HLA molecule (e.g., class I or class II) and a T-cell receptor. In various embodiments, all of the nucleic acids in a multi-epitope construct can encode class I HLA epitopes or class II HLA epitopes. Multi-epitope constructs comprising epitopes that interact exclusively with class I HLA molecules may be referred to as “CTL multi-epitope constructs” (or “CD8⁺ T cell multi-epitope constructs”). Multi-epitope constructs comprising epitopes that interact exclusively with class II HLA molecules may be referred to as “HTL multi-epitope constructs” (or “CD4⁺ T cell multi epitope constructs”). Some multi-epitope constructs (designated “TL multi-epitope constructs”) can have a subset of the multi-epitope nucleic acids encoding class I HLA epitopes and another subset of the multi-epitope nucleic acids encoding class II HLA epitopes (e.g., the constructs stimulate both CTL (i.e., CD8⁺ T cell) and HTL (i.e., CD4⁺ T cell) of the immune system). Other multi-epitope constructs can provide epitopes that interact exclusively with B-cells or immunoglobulin molecules and are designated “BL multi-epitope constructs”. Multi-epitope constructs that provide epitopes that interact with B-cells (and/or immunoglobulin molecules) and further provide class I HLA epitopes and class II HLA epitopes are designated “immune system (IMS) multi-epitope constructs”. In certain embodiments, multi-epitope constructs can provide class I or class II epitopes (e.g., CTL (i.e., CD8⁺ T cell) epitopes or HTL (ie., CD4⁺ T cell) epitopes) and BL epitopes. “Human Leukocyte Antigen” or “HLA” is a human class I or class II Major Histocompatibility Complex (MHC) protein (see, e.g., Stites, et al., IMMUNOLOGY, 8^(TH) ED., Lange Publishing, Los Altos, Calif. (1 994)).

CTL epitope (class I epitope) (i.e., CD8⁺ T cell epitope) encoding nucleic acids preferably provide an epitope peptide of about eight to about thirteen amino acids in length (e.g., 8, 9, 10, 11, 12 or 13), more preferably about eight to about eleven amino acids in length, and most preferably about nine amino acids in length. HTL (CD4⁺ T-cell) epitope nucleic acids can provide an epitope peptide of about seven to about twenty three (e.g., 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or 23) preferably about seven to about seventeen (e.g., 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or 17, more preferably about eleven to about fifteen (e.g., 11, 12, 13, 14 or 15), and most preferably about thirteen amino acids in length.

“Degenerate binding” indicates that a peptide is bound by more than one HLA molecule; a synonym is “cross reactive binding.” “Cross reactive binding” may also be used to define the interaction of an antigen with multiple populations of antibodies. In certain preferred embodiments, epitopes disclosed herein do not exhibit cross reactive or degenerate binding. Other embodiments encompass degenerate or cross reactive binding of antigens or epitopes.

With regard to a particular amino acid sequence, an “epitope” is a set of amino acid residues that is involved in recognition by a particular immunoglobulin, or in the context of T cells, those residues necessary for recognition by T cell receptor proteins and/or Major Histocompatibility Complex (MHC) receptors. In an immune system setting, in vitro or in vivo, an epitope is the collective features of a molecule, such as primary, secondary and tertiary peptide structure, and charge, that together form a site recognized by an immunoglobulin, T cell receptor or HLA molecule. Throughout this disclosure epitope and peptide are often used interchangeably. It is to be appreciated, however, that isolated or purified protein or peptide molecules larger than and comprising an epitope of the invention are still within the bounds of the invention.

A “flanking” or “linking” residue is a residue that is positioned next to an epitope. A flanking residue can be introduced or inserted at a position adjacent to the N-terminus or the C-terminus of an epitope. Flanking residues suitable for use in the subject invention are disclosed, for example, in U.S. Pat. Nos. 6,419,931, which is hereby incorporated by reference in its entirety, including all sequences, figures, references, and tables.

An “immunogenic peptide” or “peptide epitope” is a peptide that comprises an allele-specific motif or supermotif such that the peptide will bind an HLA molecule and induce a CTL (or CD8⁺ T cell) and/or HTL (or CD4⁺ T cell) response. An “immunogenic peptide” or “peptide epitope” can also be a peptide that comprises a motif that binds to antibody molecules or B-cells found in the immune system of an individual. Thus, immunogenic peptides of the invention are capable of binding to an antibody molecule, a B-cell, or appropriate HLA molecule and thereafter inducing an immune response (e.g., the induction of antibody production, a cytotoxic T cell response, or a helper T cell response) to the antigen from which the immunogenic peptide is derived.

The term “residue” refers to an amino acid or amino acid mimetic incorporated into a peptide or protein by an amide bond or amide bond mimetic.

A “spacer” or “linker” refers to a sequence that is inserted between two epitopes in a multi-epitope construct to prevent the occurrence of junctional epitopes and/or to increase the efficiency of processing. A multi-epitope construct may have one or more spacer nucleic acids. A spacer nucleic acid may flank each epitope nucleic acid in a construct, or the spacer nucleic acid to epitope nucleic acid ratio may be about 2 to 10, about 5 to 10, about 6 to 10, about 7 to 10, about 8 to 10, or about 9 to 10, where a ratio of about 8 to 10 has been determined to yield favorable results for some constructs. The spacer nucleic acid may encode one or more amino acids. A spacer nucleic acid flanking a class I HLA epitope in a multi-epitope construct is preferably between one and about eight amino acids in length. A spacer nucleic acid flanking a class II HLA epitope in a multi-epitope construct is preferably greater than five, six, seven, or more amino acids in length, and more preferably five or six amino acids in length. The number of spacers in a construct, the number of amino acids in a spacer, and the amino acid composition of a spacer can be selected to optimize epitope processing and/or minimize junctional epitopes. It is preferred that spacers are selected by concomitantly optimizing epitope processing and junctional motifs. Suitable amino acids for optimizing epitope processing are described herein. Also, suitable amino acid spacing for minimizing the number of junctional epitopes in a construct are described herein for class I and class II HLAs. For example, spacers flanking class II HLA epitopes preferably include G, P, and/or N residues as these are not generally known to be primary anchor residues (see, e.g., PCT/US00/19774). A particularly preferred spacer for flanking a class II HLA epitope includes alternating G and P residues, for example, (GP)_(n), (PG)_(n), (GP)_(n)G, or (PG)_(n)P, and so forth, where n is an integer between one and ten, preferably two or about two, and where a specific example of such a spacer is GPGPG.

In some multi-epitope constructs, it is sufficient that each spacer nucleic acid encodes the same amino acid sequence. In multi-epitope constructs having two spacer nucleic acids encoding the same amino acid sequence, the spacer nucleic acids encoding those spacers may have the same or different nucleotide sequences, where different nucleotide sequences may be preferred to decrease the likelihood of unintended recombination events when the multi-epitope construct is inserted into cells.

In other multi-epitope constructs, one or more of the spacer nucleic acids may encode different amino acid sequences. While many of the spacer nucleic acids may encode the same amino acid sequence in a multi-epitope construct, one, two, three, four, five or more spacer nucleic acids may encode different amino acid sequences, and it is possible that all of the spacer nucleic acids in a multi-epitope construct encode different amino acid sequences. Spacer nucleic acids may be optimized with respect to the epitope nucleic acids they flank by determining whether a spacer sequence will maximize epitope processing and/or minimize junctional epitopes, as described herein.

Multi-epitope constructs may be distinguished from one another according to whether the spacers in one construct optimize epitope processing or minimize junctional epitopes over another construct, and preferably, constructs may be distinguished where one construct is concomitantly optimized for epitope processing and junctional epitopes over the other. Computer assisted methods and in vitro and in vivo laboratory methods for determining whether a construct is optimized for epitope processing and junctional motifs are described herein.

“Multi-epitope constructs of the invention may also be “optimized”. The term “optimized” or “optimizing” refers to increasing the immunogenicity or antigenicity of a multi-epitope construct having at least one epitope pair by sorting epitopes to minimize the occurrence of junctional epitopes, inserting flanking residues that flank the C-terminus or N-terminus of an epitope, and inserting spacer residue to further prevent the occurrence of junctional epitopes or to provide a flanking residue. An increase in immunogenicity or antigenicity of an optimized multi-epitope construct is measured relative to a multi-epitope construct that has not been constructed based on the optimization parameters and is using assays known to those of skill in the art, e.g., assessment of immunogenicity in HLA transgenic mice, ELISPOT, interferon-gamma release assays, tetramer staining, chromium release assays, and presentation on dendritic cells.

The subject invention also concerns antibodies that bind to polypeptides of the invention. Antibodies that are immunospecific for the malarial polypeptides set forth herein are specifically contemplated. In various embodiments, antibodies which do not cross react with other proteins or malarial proteins are also specifically contemplated. The antibodies of the subject invention can be prepared using standard materials and methods known in the art (see, for example, Monoclonal Antibodies: Principles and Practice, 1983; Monoclonal Hybridoma Antibodies: Techniques and Applications, 1982; Selected Methods in Cellular Immunology, 1980; Immunological Methods, Vol. II, 1981; Practical Immunology, and Kohler et al. [1975] Nature 256:495).

The term “antibody” is used in the broadest sense and specifically covers monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired biological activity, particularly neutralizing activity. “Antibody fragments” comprise a portion of a full length antibody, generally the antigen binding or variable region thereof. Examples of antibody fragments include Fab, Fab′, F(ab′)₂, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multi-specific antibodies formed from antibody fragments.

The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to conventional (polyclonal) antibody preparations that typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler et al. [1975] Nature 256: 495, or may be made by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567). The “monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson et al. [1991] Nature 352: 624-628 and Marks et al. [1991] J. Mol. Biol. 222: 581-597, for example.

The monoclonal antibodies described herein specifically include “chimeric” antibodies (immunoglobulins) in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Pat. No. 4,816,567; and Morrison et al. [1984] Proc. Natl. Acad Sci. USA 81: 6851-6855). Also included are humanized antibodies, such as those taught in U.S. Pat. Nos. 6,407,213 or 6,417,337 which are hereby incorporated by reference in their entirety.

“Single-chain Fv” or “sFv” antibody fragments comprise the V_(H) and V_(L) domains of an antibody, wherein these domains are present in a single polypeptide chain. Generally, the Fv polypeptide further comprises a polypeptide linker between the V_(H) and V_(L) domains which enables the sFv to form the desired structure for antigen binding. For a review of sFv see Pluckthun in The Pharmacology of Monoclonal Antibodies [1994] Vol. 113:269-315, Rosenburg and Moore eds. Springer-Verlag, New York.

The term “diabodies” refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy chain variable domain (V_(H)) connected to a light chain variable domain (V_(L)) in the same polypeptide chain (V_(H)-V_(L)). Diabodies are described more fully in, for example, EP 404,097; WO 93/11161; and Hollinger et al. [1993] Proc. Natl. Acad. Sci. USA 90: 6444-6448. The term “linear antibodies” refers to the antibodies described in Zapata et al. [1995] Protein Eng. 8(10):1057-1062.

An “isolated” antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes. In preferred embodiments, the antibody will be purified (1) to greater than 95% by weight of antibody as determined by the Lowry method, and most preferably more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using Coomassie blue or, preferably, silver stain. Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.

The terms “comprising”, “consisting of” and “consisting essentially of” are defined according to their standard meaning. The terms may be substituted for one another throughout the instant application in order to attach the specific meaning associated with each term. The phrases “isolated” or “biologically pure” refer to material that is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment. “Link” or “join” refers to any method known in the art for functionally connecting peptides, including, without limitation, recombinant fusion, covalent bonding, disulfide bonding, ionic bonding, hydrogen bonding, and electrostatic bonding.

Following are examples which illustrate procedures for practicing the invention. These examples should not be construed as limiting. All percentages are by weight and all solvent mixture proportions are by volume unless otherwise noted.

In this disclosure, “binding data” results are often expressed in terms of “IC₅₀'s.” IC₅₀ is the concentration of peptide in a binding assay at which 50% inhibition of binding of a reference peptide is observed. Given the conditions in which the assays are run (i.e., limiting HLA proteins and labeled peptide concentrations), these values approximate KD values. Assays for determining binding are described in detail, e.g., in PCT publications WO 94/20127 and WO 94/03205 (each of which is hereby incorporated by reference in its entirety). It should be noted that IC₅₀ values can change, often dramatically, if the assay conditions are varied, and depending on the particular reagents used (e.g., HLA preparation, etc.). For example, excessive concentrations of HLA molecules will increase the apparent measured IC₅₀ of a given ligand. Alternatively, binding is expressed relative to a reference peptide. Although as a particular assay becomes more, or less, sensitive, the IC₅₀'s of the peptides tested may change somewhat, the binding relative to the reference peptide will not significantly change. For example, in an assay run under conditions such that the IC₅₀ of the reference peptide increases 10-fold, the IC₅₀ values of the test peptides will also shift approximately 10-fold. Therefore, to avoid ambiguities, the assessment of whether a peptide is a good, intermediate, weak, or negative binder is generally based on its IC₅₀, relative to the IC₅₀ of a standard peptide. Binding may also be determined using other assay systems including those using: live cells (e.g., Ceppellini et al., Nature 339:392, 1989; Christnick et al., Nature 352:67, 1991; Busch et al., Int. Immunol. 2:443, 19990;Hill et al., J. Immunol. 147:189,1991;del Guercio et al., J. Immunol. 154:685, 1995), cell free systems using detergent lysates (e.g., Cerundolo et al., J. Immunol. 21:2069, 1991), immobilized purified MHC (e.g., Hill et al., J. Immunol. 152, 2890, 1994; Marshall et al., J. Immunol. 152:4946, 1994), ELISA systems (e.g., Reay et al., EMBO J. 11:2829, 1992), surface plasmon resonance (e.g., Khilko et al., J. Biol. Chem. 268:15425, 1993); high flux soluble phase assays (Hammer et al., J. Exp. Med. 180:2353, 1994), and measurement of class I MHC stabilization or assembly (e.g., Ljunggren et al., Nature 346:476, 1990; Schumacher et al., Cell 62:563, 1990; Townsend et al., Cell 62:285, 1990; Parker et al., J. Immunol. 149:1896, 1992). Predicted IC₅₀ values may be referred to as PIC values and measured IC₅₀ values may be referred to a MIC values.

EXAMPLE 1

Starting with 27 open reading frames defined by Multidimensional Protein Identification Technology, 9 highly antigenic proteins were identified. These highly antigenic proteins were recognized by volunteers immunized with irradiated sporozoites; mock immunized individuals (controls) failed to recognize these proteins. Several of these nine proteins were more antigenic than previously well-characterized proteins.

To identify and prioritize a set of ORFs representing antigens potentially expressed in the sporozoite and intrahepatic stage of the parasite life cycle, MS/MS spectra of peptide sequences generated by Multidimensional Protein Identification Technology (MudPIT) (Washburn, M. P., Wolters, D., & Yates, J. R. 3^(rd). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247 (2001)) of P. falciparum sporozoite preparations were scanned against the P. falciparum genomic sequence database using SEQUEST™ software (Florens, L. et al. A proteomic view of the Plasmodium falciparum life cycle. Submitted). A panel of 27 ORF's (10 expressed only in sporozoites, and 17 common to other stages of the parasite life cycle) were selected. Their size ranged between 96-4544 amino acids (mean 1252), the percentage of the protein covered by identified peptides ranged between 0.5-49.5%, and the frequency of recognition in the P. falciparum proteome dataset ranged between 16 peptide hits from 6 different sporozoite runs (antigen 2) to single peptide hits (antigens 1, 11, 14, 16, 19 and 25. When searched against the final P. falciparum database using refined gene model predictions, and taking into consideration genomic sequence information from the Anopheles (vector) and human (host) databases, 19 of the 27 antigens could be identified using stringent selection criteria and six others could be identified only with relaxed criteria.

Amino acid sequences from the 27 ORFs were scanned with HLA-A1, A2, A3/A11, A24 and DR supertype PIC algorithms; a total of 3241 peptides were identified (range=14-435; mean=120 sequences per antigen). A set of 1142 sequences was synthesized (range=13-50; mean=42), selecting the top 10 scorers per supertype per antigen for larger ORFs. Control sets of peptides were synthesized from 4 known antigens (PfCSP, PfSSP2, PfLSA1 and PfEXP1). Next, predicted epitopes were tested for their capacity to induce recall IFN-γ immune responses using PBMC from volunteers immunized with irradiated P. falciparum sporozoites and either protected (n=4) or not protected (n=4) against challenge with infectious sporozoites, or control volunteers mock immunized in parallel (n=4) (see Table 1). Peptides were tested as pools, at 1 μg/ml each peptide with each antigen represented by a separate pool, by IFN-γ ELIspot (Washburn, M. P., Wolters, D., & Yates, J. R. 3^(rd). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247 (2001)). Positive and negative control epitopes from well characterized antigens (CMV, Influenza, EBV, HIV) were also included.

Considering a stimulation index (ratio test response/control) >2.0 as positive, 19 of the 27 unknown antigens were recognized by at least 1 of 8 irradiated sporozoite immunized volunteers, but not by any of the 4 mock immunized controls (Table 1). Nine of the 27 antigens (#2, 5, 3, 18, 22, 21, 13, 11, 20) were recognized by at least 50% of irradiated sporozoite volunteers in at least 25% of assays, 3 antigens (#1, 12, 17) were recognized by at least 25% of volunteers in at least 15% of assays, and 7 antigens (#6, 7, 9, 14, 15, 16, 19) were recognized by at least 10% volunteers in at least 5% of assays. Eight of the 27 unknown antigens (#4, 8, 10, 23, 24, 25, 26, 27) failed to induce IFN-γ responses of sufficient magnitude to meet our criteria of positivity. Pools of predicted epitopes from the known antigens, PfCSP, PfSSP2, PfLSA1 and PfEXP1, were also recognized by irradiated sporozoite volunteers although the frequency of response to those pools was somewhat lower than that to pools of peptides representing previously validated epitopes derived from the same antigens (Doolan, D. L. et al. Degenerate cytotoxic T cell epitopes from P. falciparum restricted by multiple HLA-A and HLA-B supertype alleles. Immunity. 7, 97-112 (1997); Doolan, D. L. et al. HLA-DR-promiscuous T cell epitopes from Plasmodium flaciparum pre-erthrocytic-stage antigens restricted by multiple HLA class II alleles. J Immunol. 165:1123-1137 (2000); Wang, R., et al. Induction of CD4(+) T cell-dependent CD8(+) type 1 responses in humans by a malaria DNA vaccine. Proc. Natl. Acad Sci. U.S.A. 98, 10817-10822 (2001)) (Table 1). Particularly noteworthy, the reactivity against several of the newly identified antigens greatly exceeded the reactivities observed against all 4 known antigens For example, both antigens 2 and 5 were recognized by 7/8 irradiated sporozoite volunteers in 9/16 assays, and antigens 3 and 18 were recognized by 6/8 irradiated sporozoite volunteers in 6/16 assays.

Results show that HLA-A2 peptide pools from antigens 2, 5 and 13, and HLA-A1 and HLA-DR peptide pools from antigens 2 and 5, are recognized by irradiated sporozoite volunteers who express the respective HLA alleles, but not by mock immunized controls. Deconvolution at the level of individual epitopes is in progress. Additionally, a comprehensive analysis of HLA binding against the A1, A2, A3/11, A24, and DR1 supertypes has been completed for selected antigens. Several degenerate binders have been identified for each supertype/antigen combination, and 50 to 70% of the predicted peptides have been identified as degenerate HLA binders. Further analysis also revealed that the antigenicity results correlate to a large degree with the proteomic data. For example, of 9 antigens associated with high immune reactivity, 7 were identified by multiple peptide hits in multiple MudPIT runs

All patents, patent applications, provisional applications, polynucleotide sequences, amino acid sequences, tables and publications referred to or cited herein are incorporated by reference in their entirety, including all figures, to the extent they are not inconsistent with the explicit teachings of this specification. It should be understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application. TABLE 1 Summary of immune reactivities against the panel of 27 putative antigens and 4 known antigens. MOCK IRRADIATED SPOROZOITE IMMUNIZED IMMUNIZED # vol % vol # % SI SFC # vol # Antigen respond respond assays assays respond respond respond assays  1 3 37.5 3 18.75 2.5 59.3 0 0  2 8 100   9 56.25 2.9 110.4  0 0  3 6 75   6 37.5  2.6 119.1  0 0  4 0 — — — — — 0 0  5 7 87.5 9 56.25 2.8 101.8  0 0  6 1 12.5 1  6.25 2.4 88.3 0 0  7 1 12.5 1  6.25 2.1 43.3 0 0  8 0 — — — — — 0 0  9 2 25   2 12.5  2.5 32.0 0 0 10 0 — — — — — 0 0 11 4 50   4 25   3.1 81.3 0 0 12 3 37.5 3 18.75 2.2 48.2 0 0 13 4 50   5 31.25 2.9 92.2 0 0 14 1 12.5 1  6.25 2.2 55.3 0 0 15 2 25   2 12.5  2.5 28.8 0 0 16 2 25   2 12.5  2.2 27.2 0 0 17 3 37.5 3 18.75 2.4 57.6 0 0 18 6 75   6 37.5  2.2 58.4 0 0 19 2 25   2 12.5  2.7 31.3 0 0 20 4 50   4 25   2.5 74.8 0 0 21 4 50   5 31.25 2.3 48.2 0 0 22 5 62.5 5 31.25 2.9 108.4  0 0 23 0 — — — — — 0 0 24 0 — — — — — 0 0 25 0 — — — — — 0 0 26 0 — — — — — 0 0 27 0 — — — — — 0 0 TOTAL UNKNOWNS 1-8 44.7   3.8 24.0  2.5 66.6 “HIGH” 4-8 66.7   5.9 36.8  2.7 88.3 “INTERMEDIATE” 3 37.5   3.0 18.8  2.4 55.0 “LOW” 1-2 19.6   1.6 9.8 2.4 43.8 Range 1-8 12.5-100  1-9 6.25-56.25 2.1-3.1 27.2-110.4 KNOWNS (@1 ug/ml) predicted   1.4 17.2   1.4 8.6 2.9 57.3 Range 1-3 12.5-37.5 1-3 6.25-18.75 2.0-3.4 30.5-137.4 KNOWNS (@1 ug/ml) validated   4.0 50.0   3.8 23.4  3.5 64.0 Range 3-5 37.5-62.5 3-6 18.75-37.5  3.5-3.6 46.6-91.4  TOTAL KNOWNS (@1 ug/ml)   2.3 28.1   2.2 13.5  3.2 60.0 Range 1-5 12.5-62.5 1-6 6.25-37.5  2.0-3.6 30.5-137.4 TOTAL KNOWNS (@10 ug/ml) 4-8 81.3   7.8 60.9  11.1  588.2  CMV/EBV/Flu 7 87.5  12.0 50.0  4.0 59.0 4 100

TABLE 2 Pf-derived A1 supertype peptides with PIC <20 nM PIC Accession Peptide A*0101 A*2402 Malaria locus Addn Source info No. Position No. Sequence AA PIC A*0201 A*1101 PIC 331.t00003 Chromosome10 216 98.0038 KTNKWEDIY 9 15.962 1000000.0 1475.7 1000000.0 331.t00003 Chromosome10 790 98.0039 KSIYIFYTY 9 10.624 1000000.0 34.6 1000000.0 331.t00003 Chromosome10 986 98.0040 GTFTFQNMY 9 6.439 1000000.0 51.0 1000000.0 331.t00003 Chromosome10 1298 98.0041 CNDGNILYY 9 5.246 1000000.0 1000000.0 1000000.0 331.t00003 Chromosome10 1379 98.0042 YFECIMKLY 9 8.786 1000000.0 39035.2 242.6 331.t00003 Chromosome10 1389 98.0043 VYEGKLKKY 9 18.802 1000000.0 1000000.0 1753.1 331.t00003 Chromosome10 1650 98.0001 VVDLFCGVGY 10 9.498 1000000.0 153.7 1000000.0 331.t00003 Chromosome10 1770 98.0044 FSSINTYDY 9 4.161 1000000.0 4680.1 1000000.0 331.t00003 Chromosome10 1803 98.0045 VSNVEDSNY 9 18.299 1000000.0 11308.4 1000000.0 331.t00003 Chromosome10 1831 98.0046 NSNYNKKLY 9 19.200 1000000.0 4533.0 1000000.0 18.000811 Chr12Contig18 182 98.0047 KVSDEIWNY 9 6.117 1000000.0 40.5 1000000.0 MY924Fe3.p1t1 92 98.0048 ISGEGLIIY 9 4.901 1000000.0 2464.4 1000000.0 MY924Fe3.p1t1 215 98.0002 FVEDSSSFLY 10 8.740 1000000.0 445.2 1000000.0 MY924Fe3.p1t1 384 98.0049 DSDSSNVLY 9 7.960 1000000.0 22156.1 1000000.0 MY924Fe3.p1t1 561 98.0050 SQDVFIIEY 9 6.978 1000000.0 117.2 1000000.0 MY924Fe3.p1t1 1028 98.0051 NSMFHIIMY 9 4.429 1000000.0 243.3 1000000.0 MY924Fe3.p1t1 1093 98.0052 SSYNLFEEY 9 6.022 1000000.0 82.2 1000000.0 MY924Fe3.p1t1 1258 98.0053 SSGKTFICY 9 2.145 1000000.0 264.3 1000000.0 MY924Fe3.p1t1 1340 98.0054 ILENILLSY 9 3.307 1000000.0 8368.7 1000000.0 MY924Fe3.p1t1 1439 98.0055 FSDLILYVY 9 2.218 1000000.0 4308.8 1000000.0 MY924Fe3.p1t1 2318 98.0056 HIENILLKY 9 2.560 1000000.0 10911.0 1000000.0 MP03001 MAL3P2.11 CAB38998 14 98.0057 FVEALFQEY 9 1.370 1000000.0 698.4 1000000.0 MP03001 MAL3P2.11 CAB38998 310 98.0058 PSDKHIKEY 9 18.149 1000000.0 150075.4 1000000.0 1369.t00001 Chromosome 11 38 98.0059 IMNHLMTLY 9 9.966 1000000.0 224.2 1019.1 1369.t00001 Chromosome 11 149 98.0060 LIENELMNY 9 18.117 1000000.0 15763.1 1000000.0 1369.t00001 Chromosome 11 182 98.0061 NVDQQNDMY 9 6.934 1000000.0 6419.6 1000000.0 1369.t00001 Chromosome 11 309 98.0062 SSFFMNRFY 9 17.546 1000000.0 48.4 1000000.0 1369.t00001 Chromosome 11 342 98.0063 NHEQKLSEY 9 16.912 1000000.0 1000000.0 1000000.0 1369.t00001 Chromosome 11 347 98.0003 LSEYYDXDIY 10 18.838 1000000.0 3608.2 1000000.0 1369.t00001 Chromosome 11 363 98.0064 QEEQKKYIY 9 19.642 1000000.0 1000000.0 1000000.0 699.t00001 Chromosome 11 313 98.0065 DSQNELTNY 9 19.647 1000000.0 97274.6 1000000.0 699.t00001 Chromosome 11 441 98.0004 FSFFFSLIDY 10 1.491 1000000.0 319.3 1000000.0 699.t00001 Chromosome 11 480 98.0066 CHEMKAEFY 9 15.998 1000000.0 1000000.0 1000000.0 699.t00001 Chromosome 11 548 98.0067 MFSSIFENY 9 6.908 1000000.0 1357.8 2826.7 699.t00001 Chromosome 11 749 98.0068 NSLILLNLY 9 11.791 1000000.0 4626.8 1000000.0 699.t00001 Chromosome 11 859 98.0069 YIDNDINIY 9 12.867 1000000.0 52350.4 1000000.0 699.t00001 Chromosome 11 919 98.0070 EEDKTYELY 9 13.159 1000000.0 1000000.0 1000000.0 699.t00001 Chromosome 11 922 98.0071 KTYELYQKY 9 7.495 1000000.0 22.4 1000000.0 699.t00001 Chromosome 11 1013 98.0072 CTHISYYKY 9 14.092 1000000.0 406.1 1000000.0 699.t00001 Chromosome 11 1046 98.0005 FVDEEGEQLY 10 6.559 1000000.0 5771.7 1000000.0 M13Hg2.q1t3 8 98.0073 NSLYNKIEY 9 19.553 1000000.0 3889.9 1000000.0 M13Hg2.q1t3 46 98.0006 YSSASESNFY 10 12.365 1000000.0 5058.0 1000000.0 M13Hg2.q1t3 49 98.0074 ASESNFYKY 9 1.848 1000000.0 630.5 1000000.0 M13Hg2.q1t3 196 98.0075 ASGKLFSLY 9 2.466 1000000.0 266.9 1000000.0 M13Hg2.q1t3 237 98.0076 GSNKVSDWY 9 16.782 1000000.0 1646.1 1000000.0 M13Hg2.q1t3 511 98.0007 FQDNYLKLDY 10 7.493 1000000.0 19742.1 1000000.0 M13Hg2.q1t3 597 98.0008 FFDYNSQYYY 10 19.854 1000000.0 2749.2 1043.1 M13Hg2.q1t3 597 98.0077 FFDYNSQYY 9 11.735 1000000.0 3766.2 160.3 M13Hg2.q1t3 699 98.0078 MLEQKLSNY 9 1.204 1000000.0 13925.8 1000000.0 M13Hg2.q1t3 882 98.0079 NSFNNSNIY 9 16.821 1000000.0 5231.6 1000000.0 Mal_5L10c4.q1t6 8 98.0080 CSSTKDLNY 9 2.097 1000000.0 16168.9 1000000.0 Mal_5L10c4.q1t6 263 98.0081 YDDDKYNKY 9 7.997 1000000.0 98918.2 1000000.0 Mal_5L10c4.q1t6 638 98.0082 GTYGNMENY 9 2.825 1000000.0 209.0 1000000.0 Mal_5L10c4.q1t6 690 98.0083 FTYYSCKNY 9 6.979 1000000.0 257.7 1000000.0 Mal_5L10c4.q1t6 1022 98.0084 YDERNTLVY 9 5.181 1000000.0 47876.1 1000000.0 Mal_5L10c4.q1t6 1387 98.0085 STDDSKNVY 9 4.783 1000000.0 2220.4 1000000.0 Mal_5L10c4.q1t6 1451 98.0086 FSDDNKNLY 9 2.622 1000000.0 56737.7 1000000.0 Mal_5L10c4.q1t6 1508 98.0009 YLDNELTINY 10 6.162 1000000.0 7177.6 1000000.0 Mal_5L10c4.q1t6 1709 98.0087 STTSLNYHY 9 7.670 1000000.0 19.1 1000000.0 Mal_5L10c4.q1t6 1907 98.0088 GLDLKMTLY 9 2.747 1000000.0 5170.0 1000000.0 571.t00003 Chromosome11 1044 98.0010 YTFQNNNDFY 10 2.179 1000000.0 93.5 1000000.0 571.t00003 Chromosome11 1080 98.0089 HTNNKTSIY 9 4.189 1000000.0 1677.3 1000000.0 571.t00003 Chromosome11 1710 98.0090 FVDPNKYIY 9 2.171 1000000.0 6898.3 1000000.0 571.t00003 Chromosome11 1827 98.0011 NVEAYHNDNY 10 5.835 1000000.0 1804.6 1000000.0 571.t00003 Chromosome11 1858 98.0091 YSNNSHAEY 9 7.282 1000000.0 662.3 1000000.0 571.t00003 Chromosome11 1905 98.0092 LTNNSSYIY 9 7.415 1000000.0 186.2 1000000.0 571.t00003 Chromosome11 2211 98.0093 SSSIYNQNY 9 6.330 1000000.0 318.5 1000000.0 571.t00003 Chromosome11 2476 98.0094 GSYGTFLKY 9 1.127 1000000.0 151.7 1000000.0 571.t00003 Chromosome11 2532 98.0095 DIDKTVLHY 9 4.678 1000000.0 10960.5 1000000.0 571.t00003 Chromosome11 2571 98.0012 FNDTQKKGTY 10 7.668 1000000.0 1000000.0 1000000.0 MP03072 PFC0450w CAA15614 95 98.0013 LSASDEYEQY 10 14.664 1000000.0 11938.7 1000000.0 MP03072 PFC0450w CAA15614 96 98.0096 SASDEYEQY 9 16.603 1000000.0 163.8 1000000.0 45.t00001 Chromosome14 13 98.0014 FQAAESNERY 10 13.667 1000000.0 5804.6 1000000.0 45.t00001 Chromosome14 14 98.0097 QAAESNERY 9 7.537 1000000.0 4581.2 1000000.0 45.t00001 Chromosome14 81 98.0015 ELEASISGKY 10 17.550 1000000.0 30954.5 1000000.0 45.t00001 Chromosome14 82 98.0098 LEASISGKY 9 18.208 1000000.0 1000000.0 1000000.0 45.t00001 Chromosome14 188 98.0099 NLALLYGEY 9 12.836 1000000.0 4104.6 1000000.0 MP03137 PFC0700c CAB11150 14 98.0100 SSPLFNNFY 9 20.002 1000000.0 464.0 1000000.0 MP03137 PFC0700c CAB11150 69 98.0101 LNEQLIYTY 9 10.436 1000000.0 1000000.0 1000000.0 MP03137 PFC0700c CAB11150 145 98.0102 QNADKNFLY 9 10.234 1000000.0 1000000.0 1000000.0 MP03137 PFC0700c CAB11150 255 98.0016 FVSSIFISFY 10 10.460 1000000.0 44.6 1000000.0 MP03137 PFC0700c CAB11150 256 98.0103 VSSIFISFY 9 15.732 1000000.0 544.5 1000000.0 12.t00018 Chromosome14 112 98.0104 YSYYEPLRY 9 4.229 1000000.0 560.9 1000000.0 12.t00018 Chromosome14 250 98.0017 KSNNIIPLLY 10 8.533 1000000.0 967.3 1000000.0 12.t00018 Chromosome14 467 98.0105 SSSDEENLY 9 8.006 1000000.0 2243.6 1000000.0 12.t00018 Chromosome14 468 98.0106 SSDEENLYY 9 6.105 1000000.0 64.6 1000000.0 12.t00018 Chromosome14 607 98.0107 KSNMNNNLY 9 6.927 1000000.0 923.1 1000000.0 12.t00018 Chromosome14 626 98.0108 FYDKRFIFY 9 4.639 1000000.0 1000000.0 18.3 12.t00018 Chromosome14 696 98.0018 NVEKNFLLYY 10 7.724 1000000.0 328.7 1000000.0 12.t00018 Chromosome14 696 98.0109 NVEKNFLLY 9 0.789 1000000.0 1330.7 1000000.0 12.t00018 Chromosome14 949 98.0110 KMDSFLNVY 9 6.016 1000000.0 1384.3 151.9 12.t00018 Chromosome14 1042 98.0111 NSLIEFLFY 9 9.105 1000000.0 774.9 1000000.0 mal_BU121g9.q1c1 80 98.0112 ATYKNGNIY 9 3.423 1000000.0 290.6 1000000.0 mal_9A57b11.q1t2 226 98.0113 DEEKIFVKY 9 18.436 1000000.0 1000000.0 1000000.0 mal_BL50e8.p1ca_5 86 98.0114 HTSNDSGSY 9 7.801 1000000.0 10632.6 1000000.0 mal_BL50e8.p1ca_5 136 98.0019 FSFTVGEGKY 10 4.464 1000000.0 4191.1 1000000.0 mal_BL50e8.p1ca_5 186 98.0115 ETNNNLFIY 9 3.940 1000000.0 574.3 1000000.0 mal_BL50e8.p1ca_5 319 98.0116 HVSKHAFEY 9 3.473 1000000.0 286.4 1000000.0 mal_BL50e8.p1ca_5 387 98.0117 MSGYSSNNY 9 4.983 1000000.0 1178.7 1000000.0 mal_BL50e8.p1ca_5 460 98.0118 FMESAFVNY 9 2.609 1000000.0 3568.1 1208.1 mal_BL50e8.p1ca_5 650 98.0119 RSPCSHKLY 9 6.243 1000000.0 805.6 1000000.0 mal_BL50e8.p1ca_5 679 98.0020 FTGENNIERY 10 15.909 1000000.0 1908.1 1000000.0 mal_BL50e8.p1ca_5 777 98.0120 NTLMLKADY 9 15.648 1000000.0 6774.7 1000000.0 mal_BL50e8.p1ca_5 880 98.0121 VSSKPANEY 9 15.176 1000000.0 3405.9 1000000.0 M13S8h6.p1t_3 57 98.0122 ITYSFTVSY 9 10.960 1000000.0 25.1 1000000.0 M13S8h6.p1t_3 233 98.0123 LVETLDNLY 9 3.907 1000000.0 24044.7 1000000.0 M13S8h6.p1t_3 235 98.0124 ETLDNLYLY 9 2.901 1000000.0 801.6 1000000.0 M13S8h6.p1t_3 295 98.0125 LSAKYYISY 9 4.669 1000000.0 635.7 1000000.0 M13S8h6.p1t_3 551 98.0126 HSDIHLLNY 9 1.423 1000000.0 5008.9 1000000.0 M13S8h6.p1t_3 676 98.0021 FTSPVNIKEY 10 10.972 1000000.0 1911.2 1000000.0 M13S8h6.p1t_3 746 98.0127 YSSYSSPKY 9 5.286 1000000.0 6184.9 1000000.0 M13S8h6.p1t_3 898 98.0128 GMERNKTKY 9 7.244 1000000.0 88038.7 24764.5 M13S8h6.p1t_3 1268 98.0129 YSNIDSGKY 9 11.517 1000000.0 14325.6 1000000.0 M13S8h6.p1t_3 1488 98.0130 LIDLSCIHY 9 3.960 1000000.0 1722.8 1000000.0 585.t00002 Chromosome11 297 98.0131 CSDSSLNIY 9 2.643 1000000.0 44436.7 1000000.0 585.t00002 Chromosome11 381 98.0132 VSFDNNENY 9 7.080 1000000.0 824.4 1000000.0 585.t00002 Chromosome11 465 98.0022 YTDIIINIRY 10 1.851 1000000.0 1716.6 1000000.0 585.t00002 Chromosome11 575 98.0023 LSNIRKPLFY 10 5.132 1000000.0 3669.8 1000000.0 585.t00002 Chromosome11 741 98.0133 NVDANYCKY 9 3.822 1000000.0 813.1 1000000.0 585.t00002 Chromosome11 1021 98.0134 CVEKNNMSY 9 6.497 1000000.0 33246.6 1000000.0 585.t00002 Chromosome11 1161 98.0135 SSDGKKSEY 9 5.530 1000000.0 8369.5 1000000.0 585.t00002 Chromosome11 1219 98.0136 RSNNFFFSY 9 6.117 1000000.0 11.9 1000000.0 585.t00002 Chromosome11 1361 98.0024 FTMVYEKIKY 10 2.669 1000000.0 726.8 1000000.0 585.t00002 Chromosome11 1739 98.0137 NVDIFLHYY 9 3.691 1000000.0 42.6 1000000.0 1223.t00015 mal_9A21f9.q1t_4 387 98.0138 SSNEIHNFY 9 7.488 1000000.0 19.5 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1065 98.0139 GTKLNRTKY 9 6.438 1000000.0 9805.4 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1583 98.0025 ATVSRAGIVY 10 9.716 1000000.0 351.9 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1833 98.0140 YTLSSGTKY 9 4.847 1000000.0 1878.1 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2309 98.0141 VSEKEQQLY 9 6.585 1000000.0 56024.7 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2426 98.0142 VVDFERLRY 9 3.185 1000000.0 457.2 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2778 98.0143 FIDLYKQMY 9 5.792 1000000.0 14889.5 1000000.0 1223.t00015 mal_9A21f9.q1t_4 3445 98.0144 IVDITNVNY 9 6.389 1000000.0 1065.1 1000000.0 1223.t00015 mal_9A21f9.q1t_4 4163 98.0145 LEDVKKILY 9 9.183 1000000.0 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 4267 98.0146 SLDIPDIAY 9 9.566 1000000.0 1095.4 1000000.0 599.t00001 Chromosome11 26 98.0147 SSCQNSLNY 9 1.030 1000000.0 86.7 1000000.0 599.t00001 Chromosome11 183 98.0148 KSDITNLNY 9 4.923 1000000.0 947.1 1000000.0 599.t00001 Chromosome11 304 98.0149 ETNNGDLKY 9 6.392 1000000.0 6561.2 1000000.0 599.t00001 Chromosome11 430 98.0150 LSEDNKNRY 9 7.171 1000000.0 178412.8 1000000.0 599.t00001 Chromosome11 1018 98.0026 LLDLRKNGLY 10 3.696 1000000.0 12286.3 1000000.0 599.t00001 Chromosome11 1412 98.0027 GVDKSLKIMY 10 8.185 1000000.0 3010.4 1000000.0 599.t00001 Chromosome11 1427 98.0151 YTPTNKEMY 9 6.553 1000000.0 73406.9 1000000.0 599.t00001 Chromosome11 1516 98.0028 ESANDSTNYY 10 6.672 1000000.0 2007.1 1000000.0 599.t00001 Chromosome11 1662 98.0152 LSNSITVSY 9 9.278 1000000.0 771.6 1000000.0 599.t00001 Chromosome11 1902 98.0153 GTTQSNNIY 9 3.444 1000000.0 4003.2 1000000.0 MP01072 M1045c5.p1c.C_6 27 98.0154 SDDEIIIIY 9 11.359 1000000.0 1265.6 1000000.0 MP01072 M1045c5.p1c.C_6 41 98.0155 ISSNGKLNY 9 6.926 1000000.0 2877.4 1000000.0 MP01072 M1045c5.p1c.C_6 60 98.0156 GSIQNAYLY 9 2.697 1000000.0 389.5 1000000.0 MP01072 M1045c5.p1c.C_6 381 98.0157 GTMRNRKKY 9 1.998 1000000.0 249.1 1000000.0 MP01072 M1045c5.p1c.C_6 707 98.0158 KSLLKNYNY 9 15.958 1000000.0 419.1 1000000.0 MP01072 M1045c5.p1c.C_6 725 98.0159 NVEDTNMLY 9 9.314 1000000.0 3255.4 1000000.0 MP01072 M1045c5.p1c.C_6 1065 98.0029 NTDNKDVLNY 10 6.923 1000000.0 6127.0 1000000.0 MP01072 M1045c5.p1c.C_6 1253 98.0160 HTITISQKY 9 3.528 1000000.0 4947.2 1000000.0 MP01072 M1045c5.p1c.C_6 1257 98.0161 ISQKYTSSY 9 13.157 1000000.0 5019.1 1000000.0 MP01072 M1045c5.p1c.C_6 1336 98.0030 KTFHRILAVY 10 13.836 1000000.0 85.1 1000000.0 PIR2 T28161 228 98.0162 KTNGAEERY 9 8.691 1000000.0 326.3 1000000.0 PIR2 T28161 293 98.0163 GTVPTNLDY 9 3.979 1000000.0 793.4 1000000.0 PIR2 T28161 403 98.0031 ESSQNSPKNY 10 8.536 1000000.0 24883.8 1000000.0 PIR2 T28161 639 98.0032 QTDFQGWGHY 10 2.601 1000000.0 1349.4 1000000.0 PIR2 T28161 899 98.0164 EADFIKKMY 9 9.348 1000000.0 113941.0 1000000.0 PIR2 T28161 917 98.0165 ATICRAMKY 9 5.412 1000000.0 112.4 1000000.0 PIR2 T28161 1192 98.0033 KTDEQYNENY 10 5.386 1000000.0 1911.8 1000000.0 PIR2 T28161 1201 98.0034 YTFKNPPPQY 10 8.064 1000000.0 918.8 1000000.0 PIR2 T28161 1884 98.0166 WLEYFLDDY 9 8.602 1000000.0 35096.0 1000000.0 PIR2 T28161 2221 98.0167 ITSSSESEY 9 9.299 1000000.0 1168.0 1000000.0 55.t00004 Chromosome14 45 98.0168 YVDIGSNIY 9 3.352 1000000.0 18704.2 1000000.0 55.t00004 Chromosome14 457 98.0169 DTCKNIWNY 9 3.842 1000000.0 878.3 1000000.0 55.t00004 Chromosome14 563 98.0170 LSQGKKNTY 9 10.561 1000000.0 40514.9 1000000.0 55.t00004 Chromosome14 928 98.0171 NIDCVISPY 9 8.449 1000000.0 3464.1 1000000.0 55.t00004 Chromosome14 953 98.0172 NMDNLLFTY 9 5.144 1000000.0 413.3 6464.5 55.t00004 Chromosome14 1105 98.0035 FVDHNYNYNY 10 6.601 1000000.0 687.9 1000000.0 55.t00004 Chromosome14 1261 98.0173 HSKENQQKY 9 3.798 1000000.0 41445.3 1000000.0 55.t00004 Chromosome14 1339 98.0174 VSEGYTSTY 9 7.735 1000000.0 4760.1 1000000.0 55.t00004 Chromosome14 1358 98.0175 FMDSQNGMY 9 8.455 1000000.0 21913.6 2720.6 55.t00004 Chromosome14 1537 98.0036 NSYNDSLINY 10 12.536 1000000.0 1846.9 1000000.0 13.t00011 Chromosome14 27 98.0176 STGINEENY 9 6.590 1000000.0 838.9 1000000.0 13.t00011 Chromosome14 44 98.0177 MNETVFLDY 9 5.456 1000000.0 1000000.0 1000000.0 13.t00011 Chromosome14 77 98.0178 LTSKVWDTY 9 6.496 1000000.0 616.6 1000000.0 37.t00002 Chromosome14 10 98.0179 KHDALTYMY 9 23.541 1000000.0 1000000.0 1000000.0 37.t00002 Chromosome14 14 98.0180 LTYMYCVYY 9 10.044 1000000.0 20.3 1000000.0 674.t00001 Chromosome11 201 98.0181 NIDINDLGY 9 10.069 1000000.0 23874.2 1000000.0 674.t00001 Chromosome11 260 98.0182 ISSNQFNNY 9 6.099 1000000.0 2575.9 1000000.0 674.t00001 Chromosome11 400 98.0183 DIEPLISSY 9 14.646 1000000.0 183727.1 1000000.0 674.t00001 Chromosome11 453 98.0037 VTNNDSINNY 10 17.920 1000000.0 1310.7 1000000.0 674.t00001 Chromosome11 772 98.0184 ESGKNMEHY 9 8.198 1000000.0 75390.5 1000000.0 674.t00001 Chromosome11 868 98.0185 LKDFDMLLY 9 12.047 1000000.0 1000000.0 1000000.0 674.t00001 Chromosome11 936 98.0186 YIDVEDDDY 9 13.870 1000000.0 377275.0 1000000.0 674.t00001 Chromosome11 1001 98.0187 DMDDNYYLY 9 3.056 1000000.0 2478.6 45380.9 674.t00001 Chromosome11 1224 98.0188 YGDNNKDCY 9 19.772 1000000.0 368191.0 1000000.0 674.t00001 Chromosome11 1239 98.0189 IYDFNNNSY 9 17.735 1000000.0 1000000.0 365.4

TABLE 3 Pf-derived A24 supertype peptides with PIG <100 nM PIC Accession Peptide A*0101 A*2402 Malaria locus Addn Source info No. Position No. Sequence AA PIC A*0201 A*1101 PIC 331.t00003 Chromosome10 10 98.0206 FYKKKRNVL 9 67134.0 1000000.0 1000000.0 1.708 331.t00003 Chromosome10 110 98.0207 VYEINKNEF 9 84.1 1000000.0 1000000.0 2.011 331.t00003 Chromosome10 604 98.0208 FFVWGHDMF 9 221.0 1000000.0 1000000.0 3.642 331.t00003 Chromosome10 684 98.0209 VYNIKENFW 9 123239.4 1000000.0 1000000.0 2.687 331.t00003 Chromosome10 1108 98.0210 KYNLCHNML 9 147073.6 1000000.0 1000000.0 0.324 331.t00003 Chromosome10 1268 98.0211 FYVPIKKKL 9 172677.3 1000000.0 1000000.0 2.705 331.t00003 Chromosome10 1365 98.0212 KYEIIGNIL 9 89209.4 1000000.0 1000000.0 1.961 331.t00003 Chromosome10 1449 98.0213 FWLAIKDIF 9 173.9 1000000.0 1000000.0 1.093 331.t00003 Chromosome10 1515 98.0214 LYRRRKNLF 9 113.5 1000000.0 1000000.0 1.220 331.t00003 Chromosome10 1704 98.0215 IYIIKQNSF 9 111.6 1000000.0 1000000.0 0.256 18.000811 Chr12Contig18 5 98.0190 LFVCFLIFHF 10 672.3 1000000.0 1000000.0 19.783 18.000811 Chr12Contig18 8 98.0191 CFLIFHFFLF 10 1385.7 1000000.0 1000000.0 18.444 18.000811 Chr12Contig18 8 98.0216 CFLIFHFFL 9 106491.6 1000000.0 1000000.0 0.321 18.000811 Chr12Contig18 11 98.0217 IFHFFLFLL 9 53306.2 1000000.0 1000000.0 38.527 18.000811 Chr12Contig18 13 98.0192 HFFLFLLYIL 10 1000000.0 1000000.0 1000000.0 35.659 18.000811 Chr12Contig18 13 98.0218 HFFLFLLYI 9 24845.8 1000000.0 1000000.0 26.159 18.000811 Chr12Contig18 14 98.0219 FFLFLLYIL 9 62569.1 1000000.0 1000000.0 32.471 18.000811 Chr12Contig18 19 98.0220 LYILFLVKM 9 90645.8 1000000.0 1000000.0 63.051 18.000811 Chr12Contig18 41 98.0221 VFLVFSNVL 9 178682.3 1000000.0 1000000.0 5.555 18.000811 Chr12Contig18 160 98.0222 TYGIIVPVL 9 123562.9 1000000.0 1000000.0 3.015 MY924Fe3.p1t1 153 98.0223 FFNVFNIFF 9 45.6 1000000.0 1000000.0 0.470 MY924Fe3.p1t1 1412 98.0224 FYSWLQNVL 9 83170.3 1000000.0 1000000.0 2.428 MY924Fe3.p1t1 1435 98.0225 FYERFSDLI 9 46149.1 1000000.0 1000000.0 0.625 MY924Fe3.p1t1 1534 98.0226 VYLIQNNYI 9 615175.4 1000000.0 1000000.0 0.632 MY924Fe3.p1t1 1557 98.0227 NYMKNSFYI 9 24802.7 1000000.0 1000000.0 2.200 MY924Fe3.p1t1 1800 98.0228 VYCNYVTEI 9 160654.7 1000000.0 1000000.0 3.071 MY924Fe3.p1t1 1839 98.0229 HYEVLPYKF 9 14.6 1000000.0 1000000.0 2.621 MY924Fe3.p1t1 1846 98.0230 KFTIIVESL 9 181796.5 1000000.0 1000000.0 1.946 MY924Fe3.p1t1 2159 98.0231 FMTRAHFHI 9 9020.6 52.2 1000000.0 1.455 MY924Fe3.p1t1 2380 98.0232 FYKSKVIII 9 53263.7 1000000.0 1000000.0 0.928 MP03001 MAL3P2.11 CAB38998 11 98.0233 SFLFVEALF 9 80.3 1000000.0 1000000.0 53.045 MP03001 MAL3P2.11 CAB38998 54 98.0234 YYGKQENWY 9 73.1 1000000.0 1000000.0 49.750 MP03001 MAL3P2.11 CAB38998 369 98.0235 KMEKCSSVF 9 34.0 1000000.0 1000000.0 39.989 MP03001 MAL3P2.11 CAB38998 376 98.0236 VFNVVNSSI 9 231723.3 1000000.0 1000000.0 82.506 1369.t00001 Chromosome 11 34 98.0237 NYMKIMNHL 9 37582.2 1000000.0 1000000.0 4.875 1369.t00001 Chromosome 11 225 98.0193 SYKSSKRDKF 10 1632.7 1000000.0 1000000.0 46.746 1369.t00001 Chromosome 11 264 98.0238 TYKKKNNHI 9 90904.7 1000000.0 1000000.0 12.042 1369.t00001 Chromosome 11 277 98.0239 VYYNILIVL 9 59837.4 1000000.0 1000000.0 11.637 1369.t00001 Chromosome 11 285 98.0240 LYYLFNQHI 9 56431.2 1000000.0 1000000.0 5.598 1369.t00001 Chromosome 11 310 98.0241 SFFMNRFYI 9 56480.3 1000000.0 1000000.0 80.940 1369.t00001 Chromosome 11 316 98.0242 FYITTRYKY 9 45.2 1000000.0 1000000.0 3.968 1369.t00001 Chromosome 11 328 98.0243 KYINFINFI 9 289163.4 1000000.0 1000000.0 0.095 1369.t00001 Chromosome 11 331 98.0244 NFINFIKVL 9 610070.5 1000000.0 1000000.0 37.188 1369.t00001 Chromosome 11 380 98.0245 KYEALIKLL 9 105887.8 1000000.0 1000000.0 9.605 699.t00001 Chromosome 11 443 98.0246 FFFSLIDYF 9 118.9 1000000.0 1000000.0 1.331 699.t00001 Chromosome 11 460 98.0247 KYNIKVCEL 9 98354.1 1000000.0 1000000.0 0.429 699.t00001 Chromosome 11 487 98.0248 FYLYISFLL 9 34312.8 1000000.0 1000000.0 0.417 699.t00001 Chromosome 11 664 98.0249 FYTNNANLL 9 42910.8 1000000.0 1000000.0 0.639 699.t00001 Chromosome 11 766 98.0250 EYNPSFFYL 9 22929.4 1000000.0 1000000.0 1.772 699.t00001 Chromosome 11 845 98.0251 SFIIFKNIF 9 249.9 1000000.0 1000000.0 3.449 699.t00001 Chromosome 11 881 98.0252 LYMNFLKFI 9 34148.2 1000000.0 1000000.0 4.363 699.t00001 Chromosome 11 929 98.0253 KYLIILLYI 9 93640.1 1000000.0 1000000.0 1.034 699.t00001 Chromosome 11 1020 98.0254 KYIYIYIYI 9 215740.5 1000000.0 1000000.0 0.296 699.t00001 Chromosome 11 1024 98.0255 IYIYIFIYL 9 52331.1 1000000.0 1000000.0 2.300 M13Hg2.q1t3 135 98.0256 IYINKLSFF 9 67.4 1000000.0 1000000.0 3.329 M13Hg2.q1t3 142 98.0257 FFSIKDELF 9 27.2 1000000.0 1000000.0 14.276 M13Hg2.q1t3 156 98.0258 EFLKNNSYF 9 164.9 1000000.0 1000000.0 20.204 M13Hg2.q1t3 163 98.0259 YFNIIQQKI 9 45274.1 1000000.0 1000000.0 13.888 M13Hg2.q1t3 244 98.0260 WYCSACNFL 9 56993.5 1000000.0 1000000.0 7.339 M13Hg2.q1t3 296 98.0261 LYLINNKNL 9 150801.1 1000000.0 1000000.0 28.854 M13Hg2.q1t3 345 98.0262 TYKDANNNI 9 71978.1 1000000.0 1000000.0 29.035 M13Hg2.q1t3 521 98.0263 VYEKEKQYF 9 103.6 1000000.0 1000000.0 3.963 M13Hg2.q1t3 553 98.0194 PYFNFFVNYF 10 185.8 1000000.0 1000000.0 33.503 M13Hg2.q1t3 889 98.0264 IYNNNNEHI 9 77962.6 1000000.0 1000000.0 24.919 Mal_5L10c4.q1t6 78 98.0265 EYNKYNEYF 9 90.4 1000000.0 1000000.0 3.130 Mal_5L10c4.q1t6 137 98.0266 NYVNNNNVF 9 220.5 1000000.0 1000000.0 3.441 Mal_5L10c4.q1t6 321 98.0267 KYPIKYCEL 9 183114.8 1000000.0 1000000.0 0.364 Mal_5L10c4.q1t6 416 98.0268 AYHDLIKLF 9 66.8 1000000.0 1000000.0 4.671 Mal_5L10c4.q1t6 533 98.0269 KYISSVNYF 9 194.8 1000000.0 1000000.0 0.018 Mal_5L10c4.q1t6 773 98.0270 KYDWFFNSF 9 34.0 1000000.0 1000000.0 0.374 Mal_5L10c4.q1t6 1183 98.0271 HYVIKKYII 9 133499.1 1000000.0 1000000.0 1.507 Mal_5L10c4.q1t6 1259 98.0272 LYLHIHKLF 9 72.0 1000000.0 1000000.0 0.343 Mal_5L10c4.q1t6 1323 98.0273 YYRTNYGYI 9 165642.6 1000000.0 1000000.0 4.072 Mal_5L10c4.q1t6 2054 98.0274 KYLRYHSQL 9 421667.1 1000000.0 1000000.0 0.655 571.t00003 Chromosome11 74 98.0275 FYIDKCIHF 9 23.2 1000000.0 1000000.0 0.120 571.t00003 Chromosome11 162 98.0276 FYTNYYQSF 9 48.3 1000000.0 1000000.0 0.186 571.t00003 Chromosome11 177 98.0277 PYINQTNIF 9 228.9 1000000.0 1000000.0 0.527 571.t00003 Chromosome11 807 98.0278 NYPNNANHI 9 176667.0 1000000.0 1000000.0 3.103 571.t00003 Chromosome11 834 98.0279 TYNNFHNSY 9 52.4 1000000.0 1000000.0 0.776 571.t00003 Chromosome11 1917 98.0280 YMNNNTYSF 9 7.7 1000000.0 1000000.0 2.132 571.t00003 Chromosome11 2026 98.0281 KYTEGATNF 9 74.8 1000000.0 1000000.0 1.964 571.t00003 Chromosome11 2450 98.0282 FYISIIDII 9 150563.0 1000000.0 1000000.0 1.632 571.t00003 Chromosome11 2540 98.0283 YYKEHISEF 9 96.3 1000000.0 1000000.0 3.143 571.t00003 Chromosome11 2914 98.0284 YYNRANNEI 9 46291.4 1000000.0 1000000.0 3.342 MP03072 PFC0450w CAA15614 17 98.0285 AFLLITFLM 9 37258.4 1000000.0 1000000.0 17.525 MP03072 PFC0450w CAA15614 53 98.0195 LYVIFLVLLF 10 174.0 1000000.0 1000000.0 16.581 MP03072 PFC0450w CAA15614 53 98.0286 LYVIFLVLL 9 107336.6 1000000.0 1000000.0 5.089 MP03072 PFC0450w CAA15614 86 98.0287 KYVQLASTY 9 65.1 1000000.0 1000000.0 70.547 45.t00001 Chromosome14 21 98.0196 RYQDPQNYEL 10 1000000.0 1000000.0 1000000.0 46.471 45.t00001 Chromosome14 40 98.0288 IYYFDGNSW 9 97026.0 1000000.0 1000000.0 15.493 45.t00001 Chromosome14 94 98.0289 VYRHCEYIL 9 560574.8 1000000.0 1000000.0 27.538 45.t00001 Chromosome14 135 98.0290 TWKPTIFLL 9 34068.5 1000000.0 1000000.0 26.741 45.t00001 Chromosome14 168 98.0291 SYKVNCINF 9 25.3 1000000.0 1000000.0 63.592 45.t00001 Chromosome14 216 98.0292 KYNYFIHFF 9 39.1 1000000.0 1000000.0 0.380 45.t00001 Chromosome14 218 98.0293 NYFIHFFTW 9 95820.5 1000000.0 1000000.0 2.156 45.t00001 Chromosome14 222 98.0294 HFFTWGTMF 9 17.4 1000000.0 1000000.0 6.418 45.t00001 Chromosome14 229 98.0295 MFVPKYFEL 9 57423.3 1000000.0 1000000.0 28.589 45.t00001 Chromosome14 295 98.0296 IYTIIQDQL 9 334935.0 1000000.0 1000000.0 9.774 MP03137 PFC0700c CAB11150 3 98.0197 DFFLKSKFNI 10 1000000.0 1000000.0 1000000.0 79.527 MP03137 PFC0700c CAB11150 4 98.0297 FFLKSKFNI 9 80470.7 1000000.0 1000000.0 10.043 MP03137 PFC0700c CAB11150 9 98.0298 KFNILSSPL 9 275819.0 1000000.0 1000000.0 48.661 MP03137 PFC0700c CAB11150 61 98.0299 RMTSLKNEL 9 45471.5 1089.6 1000000.0 50.292 MP03137 PFC0700c CAB11150 77 98.0300 YYNNFNNNY 9 29.9 1000000.0 1000000.0 2.802 MP03137 PFC0700c CAB11150 87 98.0301 YYNKSTEKL 9 25069.1 1000000.0 1000000.0 6.131 MP03137 PFC0700c CAB11150 109 98.0302 EYEPTANLL 9 29899.8 1000000.0 1000000.0 9.359 12.t00018 Chromosome14 479 98.0303 PYEEVENYF 9 118.2 1000000.0 1000000.0 3.525 12.t00018 Chromosome14 506 98.0304 KFILHMTLL 9 418744.3 1000000.0 1000000.0 7.942 12.t00018 Chromosome14 544 98.0305 NFLNIYASL 9 309896.9 1000000.0 1000000.0 7.653 12.t00018 Chromosome14 594 98.0306 VWKKLIEYF 9 120.2 1000000.0 1000000.0 7.058 12.t00018 Chromosome14 614 98.0307 LYVSMYIPF 9 113.5 1000000.0 1000000.0 6.679 12.t00018 Chromosome14 618 98.0308 MYIPFIKKF 9 62.3 1000000.0 1000000.0 2.663 12.t00018 Chromosome14 625 98.0309 KFYDKRFIF 9 53.3 1000000.0 1000000.0 1.395 12.t00018 Chromosome14 675 98.0310 IYNMYHNNF 9 27.2 1000000.0 1000000.0 0.737 12.t00018 Chromosome14 678 98.0311 MYHNNFSYF 9 61.8 1000000.0 1000000.0 5.105 12.t00018 Chromosome14 815 98.0312 KYDITKNLI 9 86746.4 1000000.0 1000000.0 2.983 mal_BU121g9.q1c1 61 98.0313 GYFKRIFKL 9 39278.5 1000000.0 1000000.0 64.889 mal_BU121g9.q1c1 81 98.0314 TYKNGNIYI 9 240142.1 1000000.0 1000000.0 20.110 mal_BU121g9.q1c1 87 98.0315 IYIYIYIYI 9 133656.3 1000000.0 1000000.0 2.246 mal_BU121g9.q1c1 89 98.0198 IYIYIYIYFL 10 1000000.0 1000000.0 1000000.0 72.026 mal_BU121g9.q1c1 89 98.0316 IYIYIYIYF 9 89.8 1000000.0 1000000.0 0.543 mal_9A57b11.q1t2 75 98.0317 IFKNDNNTF 9 290.7 1000000.0 1000000.0 11.568 mal_9A57b11.q1t2 103 98.0318 KYGNICHHI 9 61693.1 1000000.0 1000000.0 4.552 mal_9A57b11.q1t2 139 98.0319 QYTDIPSLI 9 41835.9 1000000.0 1000000.0 24.727 mal_9A57b11.q1t2 159 98.0320 VFCYEYFIF 9 98.9 1000000.0 1000000.0 69.226 mal_9A57b11.q1t2 161 98.0199 CYEYFIFDIF 10 811.1 1000000.0 1000000.0 61.974 mal_9A57b11.q1t2 161 98.0321 CYEYFIFDI 9 32300.1 1000000.0 1000000.0 79.659 mal_9A57b11.q1t2 171 98.0322 KYARNILSL 9 27927.9 1000000.0 1000000.0 3.398 mal_9A57b11.q1t2 230 98.0323 IFVKYLPLF 9 68.2 1000000.0 1000000.0 30.518 mal_9A57b11.q1t2 233 98.0324 KYLPLFLMM 9 16925.5 1000000.0 1000000.0 15.776 mal_9A57b11.q1t2 237 98.0325 LFLMMEHSF 9 51.0 1000000.0 1000000.0 70.804 mal_BL50e8.p1ca_5 116 98.0326 QYSNYFDYL 9 103941.7 1000000.0 1000000.0 17.499 mal_BL50e8.p1ca_5 184 98.0327 PYETNNNLF 9 37.2 1000000.0 1000000.0 4.367 mal_BL50e8.p1ca_5 341 98.0328 YYSRRVEKI 9 33168.4 1000000.0 1000000.0 6.349 mal_BL50e8.p1ca_5 555 98.0329 KFKWIQDNL 9 453346.6 1000000.0 1000000.0 30.007 mal_BL50e8.p1ca_5 687 98.0200 RYVGLGSFHF 10 1143.3 1000000.0 1000000.0 33.267 mal_BL50e8.p1ca_5 768 98.0330 TYKMYPPEF 9 68.2 1000000.0 1000000.0 7.746 mal_BL50e8.p1ca_5 771 98.0331 MYPPEFNTL 9 37286.8 1000000.0 1000000.0 14.291 mal_BL50e8.p1ca_5 827 98.0332 KYCIGSTYF 9 184.3 1000000.0 1000000.0 0.261 mal_BL50e8.p1ca_5 833 98.0333 TYFLRQVSI 9 163553.3 1000000.0 1000000.0 31.623 mal_BL50e8.p1ca_5 857 98.0334 KYSARLHPI 9 52609.1 1000000.0 1000000.0 33.171 M13S8h6.p1t_3 152 98.0335 FYLKKKFLF 9 30.5 1000000.0 1000000.0 0.091 M13S8h6.p1t_3 298 98.0336 KYYISYKVL 9 328554.4 1000000.0 1000000.0 3.468 M13S8h6.p1t_3 321 98.0337 KYINKNISL 9 213679.4 1000000.0 1000000.0 0.395 M13S8h6.p1t_3 380 98.0338 KYLKEDNTF 9 189.5 1000000.0 1000000.0 2.580 M13S8h6.p1t_3 753 98.0339 KYGDNENNF 9 50.4 1000000.0 1000000.0 2.048 M13S8h6.p1t_3 1208 98.0340 VFTKINNLF 9 55.7 1000000.0 1000000.0 4.101 M13S8h6.p1t_3 1438 98.0341 IWLIRSIYL 9 175087.7 1000000.0 1000000.0 2.659 M13S8h6.p1t_3 1444 98.0342 IYLFIITYI 9 153399.4 1000000.0 1000000.0 4.385 M13S8h6.p1t_3 1536 98.0343 FFFVFFYIF 9 26.2 1000000.0 1000000.0 0.631 M13S8h6.p1t_3 1541 98.0344 FYIFLIYSF 9 60.5 1000000.0 1000000.0 0.315 585.t00002 Chromosome11 1 98.0345 MYIFFFILF 9 12.6 1000000.0 1000000.0 1.911 585.t00002 Chromosome11 11 98.0346 FYVMSTYTF 9 45.7 1000000.0 1000000.0 0.144 585.t00002 Chromosome11 512 98.0347 RYCTKCFLW 9 31357.1 1000000.0 1000000.0 1.726 585.t00002 Chromosome11 605 98.0348 VYAKNIPLW 9 36459.4 1000000.0 1000000.0 1.882 585.t00002 Chromosome11 663 98.0349 FFCIFFISL 9 35177.1 1000000.0 1000000.0 1.436 585.t00002 Chromosome11 681 98.0350 PYYKKKNLF 9 53.3 1000000.0 1000000.0 2.732 585.t00002 Chromosome11 1378 98.0351 FYTLVNILI 9 40959.2 1000000.0 1000000.0 2.113 585.t00002 Chromosome11 1419 98.0352 YFIIRSYEL 9 135598.6 1000000.0 1000000.0 2.721 585.t00002 Chromosome11 1483 98.0353 KYICLTCAF 9 30.1 1000000.0 1000000.0 0.435 585.t00002 Chromosome11 1752 98.0354 KYDLFNNFI 9 83062.5 1000000.0 1000000.0 1.355 1223.t00015 mal_9A21f9.q1t_4 1202 98.0355 KYKDMAKIF 9 215.2 1000000.0 1000000.0 0.315 1223.t00015 mal_9A21f9.q1t_4 1599 98.0356 GYRPFIYSW 9 83421.5 1000000.0 1000000.0 3.292 1223.t00015 mal_9A21f9.q1t_4 1621 98.0357 LYAIFNKLF 9 57.9 1000000.0 1000000.0 0.212 1223.t00015 mal_9A21f9.q1t_4 1631 98.0358 FYLDKIQIL 9 36632.3 1000000.0 1000000.0 0.942 1223.t00015 mal_9A21f9.q1t_4 2272 98.0359 RMEDKTFSL 9 8870.6 143.4 1000000.0 4.349 1223.t00015 mal_9A21f9.q1t_4 2702 98.0360 IYNCVTINW 9 10684.6 1000000.0 1000000.0 2.727 1223.t00015 mal_9A21f9.q1t_4 3109 98.0361 RWTDDSNNF 9 60.4 1000000.0 1000000.0 1.600 1223.t00015 mal_9A21f9.q1t_4 3735 98.0362 FFYDILNVI 9 40209.1 1000000.0 1000000.0 5.095 1223.t00015 mal_9A21f9.q1t_4 3968 98.0363 KYRKIIYSL 9 215862.1 1000000.0 1000000.0 0.665 1223.t00015 mal_9A21f9.q1t_4 4515 98.0364 KYFIFRIHL 9 114989.5 1000000.0 1000000.0 0.325 599.t00001 Chromosome11 8 98.0365 KYLTINFFI 9 160943.0 1000000.0 1000000.0 0.123 599.t00001 Chromosome11 14 98.0366 FFILLTLVF 9 30.5 1000000.0 1000000.0 3.495 599.t00001 Chromosome11 24 98.0367 KYSSCQNSL 9 213208.8 1000000.0 1000000.0 0.906 599.t00001 Chromosome11 955 98.0368 KFIEHINEF 9 278.8 1000000.0 1000000.0 1.175 599.t00001 Chromosome11 1118 98.0369 KYIELNDLI 9 231736.4 1000000.0 1000000.0 1.464 599.t00001 Chromosome11 1194 98.0370 PYSNVTYVI 9 97127.6 1000000.0 1000000.0 1.861 599.t00001 Chromosome11 1434 98.0371 MYDILNAYF 9 42.0 1000000.0 1000000.0 1.204 599.t00001 Chromosome11 1769 98.0372 HYIMNNTIF 9 38.3 1000000.0 1000000.0 1.389 599.t00001 Chromosome11 1929 98.0373 FFKYIISYF 9 126.1 1000000.0 1000000.0 3.000 599.t00001 Chromosome11 1943 98.0374 KYLNDDNYL 9 679247.8 1000000.0 1000000.0 0.368 MP01072 M1045c5.p1c.C_6 67 98.0375 LYKSIFKAF 9 52.5 1000000.0 1000000.0 21.749 MP01072 M1045c5.p1c.C_6 107 98.0376 SYRIVNAGF 9 268.7 1000000.0 1000000.0 7.480 MP01072 M1045c5.p1c.C_6 319 98.0377 KYTFRSLSI 9 63496.4 1000000.0 1000000.0 7.958 MP01072 M1045c5.p1c.C_6 388 98.0378 KYKNDSNRI 9 401700.0 1000000.0 1000000.0 6.170 MP01072 M1045c5.p1c.C_6 612 98.0379 SYIYNKNIF 9 105.6 1000000.0 1000000.0 13.043 MP01072 M1045c5.p1c.C_6 1042 98.0380 FMKNNTTLF 9 11.7 1000000.0 1000000.0 2.141 MP01072 M1045c5.p1c.C_6 1123 98.0381 HYVMINNNL 9 52910.4 1000000.0 1000000.0 3.607 MP01072 M1045c5.p1c.C_6 1163 98.0382 FFLFFSIFI 9 69264.3 1000000.0 1000000.0 2.646 MP01072 M1045c5.p1c.C_6 1249 98.0383 RYFLHTITI 9 101443.4 1000000.0 1000000.0 2.834 MP01072 M1045c5.p1c.C_6 1260 98.0384 KYTSSYDSL 9 230897.9 1000000.0 1000000.0 1.533 PIR2 T28161 243 98.0385 YYKLREDWW 9 283854.6 1000000.0 1000000.0 8.617 PIR2 T28161 304 98.0386 QYLRWFEEW 9 35188.7 1000000.0 1000000.0 14.859 PIR2 T28161 628 98.0387 HWTQIKKHF 9 30.8 1000000.0 1000000.0 11.497 PIR2 T28161 647 98.0388 HYFVLETVL 9 65432.8 1000000.0 1000000.0 12.976 PIR2 T28161 833 98.0389 RWMDTAGFI 9 32693.4 1000000.0 1000000.0 6.822 PIR2 T28161 848 98.0201 IYMPPRRQHF 10 391.2 1000000.0 1000000.0 14.666 PIR2 T28161 1024 98.0390 RWMTEWAEW 9 39609.0 1000000.0 1000000.0 3.877 PIR2 T28161 1574 98.0391 KYQYDKVKL 9 515925.0 1000000.0 1000000.0 6.877 PIR2 T28161 1681 98.0392 KYCRFYKRW 9 239673.9 1000000.0 1000000.0 3.433 PIR2 T28161 1887 98.0393 YFLDDYNKI 9 114991.6 1000000.0 1000000.0 7.588 55.t00004 Chromosome14 223 98.0394 KYELRKTSI 9 226076.9 1000000.0 1000000.0 3.213 55.t00004 Chromosome14 339 98.0395 MYKNKVDPL 9 208222.7 1000000.0 1000000.0 31.490 55.t00004 Chromosome14 455 98.0396 YYDTCKNIW 9 80910.8 1000000.0 1000000.0 11.820 55.t00004 Chromosome14 686 98.0397 KYINNMSFI 9 317672.0 1000000.0 1000000.0 1.757 55.t00004 Chromosome14 896 98.0398 LYPWKENKF 9 99.5 1000000.0 1000000.0 6.128 55.t00004 Chromosome14 973 98.0399 KWNVFNNSI 9 191824.8 1000000.0 1000000.0 0.536 55.t00004 Chromosome14 1027 98.0400 KFKIINSYI 9 648818.6 1000000.0 1000000.0 2.246 55.t00004 Chromosome14 1123 98.0401 NYAYDNIEL 9 113781.7 1000000.0 1000000.0 8.937 55.t00004 Chromosome14 1155 98.0402 IYTSTNNII 9 105468.3 1000000.0 1000000.0 7.723 55.t00004 Chromosome14 1268 98.0403 KYTYNINNL 9 65476.9 1000000.0 1000000.0 7.681 13.t00011 Chromosome14 68 98.0202 RYNVINHIYL 10 1000000.0 1000000.0 1000000.0 74.419 13.t00011 Chromosome14 68 98.0404 RYNVINHIY 9 26.0 1000000.0 1000000.0 55.779 13.t00011 Chromosome14 84 98.0405 TYNYLTPTL 9 75416.9 1000000.0 1000000.0 7.874 13.t00011 Chromosome14 96 98.0203 RFRVFKDYSF 10 3387.1 1000000.0 1000000.0 29.344 13.t00011 Chromosome14 99 98.0406 VFKDYSFFI 9 99598.3 1000000.0 1000000.0 7.373 13.t00011 Chromosome14 105 98.0407 FFIDEVKKI 9 230004.2 1000000.0 1000000.0 12.686 37.t00002 Chromosome14 20 98.0408 VYYDNYESL 9 72350.5 1000000.0 1000000.0 10.652 674.t00001 Chromosome11 68 98.0409 RFVEKIYYL 9 228887.0 1000000.0 1000000.0 8.045 674.t00001 Chromosome11 114 98.0410 IYINVQKNL 9 306183.0 1000000.0 1000000.0 14.033 674.t00001 Chromosome11 140 98.0411 KFYYYFKEF 9 92.8 1000000.0 1000000.0 14.487 674.t00001 Chromosome11 141 98.0204 FYYYFKEFLL 10 1000000.0 1000000.0 1000000.0 13.628 674.t00001 Chromosome11 141 98.0412 FYYYFKEFL 9 104311.6 1000000.0 1000000.0 1.300 674.t00001 Chromosome11 418 98.0413 TYIPDKKLL 9 209801.1 1000000.0 1000000.0 17.181 674.t00001 Chromosome11 461 98.0414 NYLYNKYYI 9 288938.1 1000000.0 1000000.0 5.750 674.t00001 Chromosome11 579 98.0415 NFKEQHLLF 9 72.4 1000000.0 1000000.0 38.780 674.t00001 Chromosome11 649 98.0416 HYINNKHNL 9 41447.1 1000000.0 1000000.0 10.887 674.t00001 Chromosome11 800 98.0417 LYREHSREL 9 274526.6 1000000.0 1000000.0 38.601 674.t00001 Chromosome11 1095 98.0418 NYINNNIYL 9 268777.1 1000000.0 1000000.0 3.259 674.t00001 Chromosome11 1117 98.0419 NYNQKENSF 9 40.2 1000000.0 1000000.0 27.868 674.t00001 Chromosome11 1396 98.0205 QYKVKIKPVF 10 5076.8 1000000.0 1000000.0 42.788

TABLE 4 Pf-derived A2 supertype peptides with PIC <100 nM PIC Accession Peptide A*0201 Malaria locus Addn Source info Position No. No. Sequence AA A*0101 PIC A*1101 A*2402 331.t00003 Chromosome10 105 99.0042 LIYPCVYEI 9 38050.5 43.8 1000000.0 1000000.0 331.t00003 Chromosome10 598 99.0043 NMNVQNFFV 9 50979.5 35.3 1000000.0 1000000.0 331.t00003 Chromosome10 605 99.0044 FVWGHDMFM 9 25516.6 18.5 1000000.0 1000000.0 331.t00003 Chromosome10 660 99.0045 QLDDKFAFI 9 3138.5 43.0 1000000.0 1000000.0 331.t00003 Chromosome10 950 99.0046 CLINHNFFM 9 63467.3 65.7 1000000.0 1000000.0 331.t00003 Chromosome10 957 99.0047 FMLVGGINI 9 11445.4 72.5 1000000.0 399.0 331.t00003 Chromosome10 1007 99.0048 YIIGGGCTV 9 19833.9 77.9 1000000.0 1000000.0 331.t00003 Chromosome10 1016 99.0049 FTFGSFFDV 9 2705.2 14.1 1000000.0 1000000.0 331.t00003 Chromosome10 1847 99.0050 NLSFAQYTL 9 22775.6 52.7 1000000.0 1000000.0 331.t00003 Chromosome10 1889 99.0051 RMYHYVVDI 9 47589.4 49.4 1000000.0 890.2 18.000811 Chr12Contig18 2 99.0001 VLRLFVCFLI 10 1000000.0 72.4 1000000.0 1000000.0 18.000811 Chr12Contig18 9 99.0002 FLIFHFFLFL 10 1000000.0 10.9 1000000.0 1000000.0 18.000811 Chr12Contig18 10 99.0003 LIFHFFLFLL 10 1000000.0 29.1 1000000.0 1000000.0 18.000811 Chr12Contig18 15 99.0004 FLFLLYILFL 10 404264.4 19.6 1000000.0 1000000.0 18.000811 Chr12Contig18 32 99.0005 RLPVICSFLV 10 1000000.0 99.3 1000000.0 1000000.0 18.000811 Chr12Contig18 35 99.0006 VICSFLVFLV 10 1000000.0 71.5 1000000.0 1000000.0 18.000811 Chr12Contig18 39 99.0007 FLVFLVFSNV 10 1000000.0 45.6 1000000.0 1000000.0 18.000811 Chr12Contig18 10 99.0052 LIFHFFLFL 9 8592.7 9.8 1000000.0 1000000.0 18.000811 Chr12Contig18 17 99.0053 FLLYILFLV 9 6742.1 1.9 1000000.0 1000000.0 18.000811 Chr12Contig18 35 99.0054 VICSFLVFL 9 43080.6 76.0 1000000.0 1000000.0 18.000811 Chr12Contig18 159 99.0055 ATYGIIVPV 9 18077.0 45.4 1000000.0 1000000.0 MY924Fe3.p1t1 222 99.0008 FLYAFNKYYV 10 538964.2 15.2 1000000.0 1000000.0 MY924Fe3.p1t1 127 99.0056 NMISVVYYI 9 97099.2 14.5 1000000.0 8.2 MY924Fe3.p1t1 299 99.0057 SLCFYFLLL 9 2719.7 20.9 1000000.0 1000000.0 MY924Fe3.p1t1 470 99.0058 ILFLHNYLL 9 31359.3 26.7 1000000.0 1000000.0 MY924Fe3.p1t1 512 99.0059 YLDVYNFLL 9 4353.0 7.2 1000000.0 1000000.0 MY924Fe3.p1t1 1209 99.0060 FQLYYMYYL 9 91212.8 4.0 1000000.0 1000000.0 MY924Fe3.p1t1 1267 99.0061 YVMDKVLRL 9 984.8 45.3 1000000.0 1000000.0 MY924Fe3.p1t1 2260 99.0062 LLFILSHFI 9 11073.4 23.7 1000000.0 1000000.0 MY924Fe3.p1t1 2326 99.0063 YLVNYCLVV 9 16842.3 10.9 1000000.0 1000000.0 MY924Fe3.p1t1 2395 99.0064 KIYVCIYYL 9 157982.7 39.3 1000000.0 1000000.0 MP03001 MAL3P2.11 6 CAB38998 99.0009 ILSVSSFLFV 10 1000000.0 94.9 1000000.0 1000000.0 MP03001 MAL3P2.11 386 CAB38998 99.0010 LIMVLSFLFL 10 1000000.0 38.4 1000000.0 1000000.0 MP03001 MAL3P2.11 318 CAB38998 99.0065 YLNKIQNSL 9 13496.2 78.4 1000000.0 1000000.0 MP03001 MAL3P2.11 387 CAB38998 99.0066 IMVLSFLFL 9 8739.3 36.0 1000000.0 2608.6 1369.t00001 Chromosome 11 60 99.0011 VQMMIMIKFM 10 1000000.0 96.6 1000000.0 1000000.0 1369.t00001 Chromosome 11 62 99.0012 MMIMIKFMGV 10 1000000.0 47.1 1000000.0 1000000.0 1369.t00001 Chromosome 11 9 99.0067 KIYKIIIWI 9 56576.0 72.2 1000000.0 1000000.0 1369.t00001 Chromosome 11 23 99.0068 YMIKKLLKI 9 4324.7 52.7 1000000.0 788.9 1369.t00001 Chromosome 11 42 99.0069 LMTLYQIQV 9 32880.1 41.7 1000000.0 1000000.0 1369.t00001 Chromosome 11 68 99.0070 FMGVIYIMI 9 10136.0 91.9 1000000.0 58.6 1369.t00001 Chromosome 11 280 99.0071 NILIVLYYL 9 117610.0 42.8 1000000.0 1000000.0 1369.t00001 Chromosome 11 312 99.0072 FMNRFYITT 9 14073.8 47.8 1000000.0 1000000.0 699.t00001 Chromosome 11 488 99.0013 YLYISFLLLI 10 311433.0 34.2 1000000.0 1000000.0 699.t00001 Chromosome 11 1025 99.0014 YIYIFIYLFI 10 1000000.0 19.8 1000000.0 1000000.0 699.t00001 Chromosome 11 408 99.0073 LLDDYHFET 9 5923.7 39.5 1000000.0 1000000.0 699.t00001 Chromosome 11 488 99.0074 YLYISFLLL 9 2547.9 11.2 1000000.0 1000000.0 699.t00001 Chromosome 11 572 99.0075 FLTLTVYPI 9 22535.9 28.3 1000000.0 1000000.0 699.t00001 Chromosome 11 651 99.0076 FIIEILELL 9 15575.2 47.0 1000000.0 1000000.0 699.t00001 Chromosome 11 782 99.0077 LLYNHITSI 9 62668.0 50.4 1000000.0 1000000.0 699.t00001 Chromosome 11 882 99.0078 YMNFLKFIV 9 14215.9 50.3 1000000.0 1000000.0 699.t00001 Chromosome 11 1033 99.0079 FIYIWLHLI 9 6243.9 15.6 1000000.0 1000000.0 699.t00001 Chromosome 11 1039 99.0080 HLIIIFIFV 9 6908.2 11.5 1000000.0 1000000.0 M13Hg2.q1t3 576 99.0015 FLMWSSQIII 10 96042.7 91.8 1000000.0 1000000.0 M13Hg2.q1t3 96 99.0081 ILLSRFIFI 9 11278.3 22.9 1000000.0 1000000.0 M13Hg2.q1t3 508 99.0082 YLNFQDNYL 9 34942.8 80.6 1000000.0 1000000.0 M13Hg2.q1t3 551 99.0083 NIPYFNFFV 9 86593.7 41.8 1000000.0 1000000.0 M13Hg2.q1t3 558 99.0084 FVNYFEAVV 9 15474.4 100.0 1000000.0 1000000.0 M13Hg2.q1t3 569 99.0085 NIHCYTYFL 9 27934.2 25.6 1000000.0 1000000.0 M13Hg2.q1t3 576 99.0086 FLMWSSQII 9 5275.5 31.9 1000000.0 1000000.0 M13Hg2.q1t3 577 99.0087 LMWSSQIII 9 15320.6 46.4 1000000.0 614.0 M13Hg2.q1t3 723 99.0088 ILNKISSFV 9 17591.1 89.9 1000000.0 1000000.0 Mal_5L10c4.q1t6 334 99.0089 FVFFIIKNV 9 13366.7 53.5 1000000.0 1000000.0 Mal_5L10c4.q1t6 366 99.0090 IQICKLYHV 9 8534.4 35.2 1000000.0 1000000.0 Mal_5L10c4.q1t6 534 99.0091 YISSVNYFL 9 25585.7 24.2 1000000.0 1000000.0 Mal_5L10c4.q1t6 1205 99.0092 YLFQLVQSL 9 4424.1 26.3 1000000.0 1000000.0 Mal_5L10c4.q1t6 1240 99.0093 SIYFYWFLL 9 13813.9 27.2 1000000.0 1000000.0 Mal_5L10c4.q1t6 1260 99.0094 YLHIHKLFI 9 46175.4 47.6 1000000.0 1000000.0 Mal_5L10c4.q1t6 1596 99.0095 ILDDSINFV 9 8148.9 41.5 1000000.0 1000000.0 Mal_5L10c4.q1t6 1629 99.0096 FLPEQSYVL 9 36294.8 55.0 1000000.0 1000000.0 Mal_5L10c4.q1t6 1890 99.0097 HLVIQIIYV 9 52344.4 36.6 1000000.0 1000000.0 Mal_5L10c4.q1t6 2106 99.0098 FLSVINASV 9 15607.8 17.1 1000000.0 1000000.0 571.t00003 Chromosome11 105 99.0016 ILYPSLMPYV 10 1000000.0 81.0 1000000.0 1000000.0 571.t00003 Chromosome11 2443 99.0017 YLFGKVKFYI 10 821413.1 47.5 1000000.0 1000000.0 571.t00003 Chromosome11 68 99.0099 KLINTNFYI 9 109718.5 49.2 1000000.0 1000000.0 571.t00003 Chromosome11 92 99.0100 KTFIYSNFL 9 34260.6 95.5 1000000.0 1000000.0 571.t00003 Chromosome11 109 99.0101 SLMPYVECI 9 3307.6 80.4 1000000.0 1000000.0 571.t00003 Chromosome11 163 99.0102 YTNYYQSFI 9 14053.9 63.6 1000000.0 1000000.0 571.t00003 Chromosome11 1224 99.0103 FQWEKSNKI 9 17731.1 88.1 1000000.0 1000000.0 571.t00003 Chromosome11 1330 99.0104 FLIKLNNEI 9 32980.5 73.6 1000000.0 1000000.0 571.t00003 Chromosome11 1478 99.0105 YMYTNYLNM 9 5105.1 65.8 1000000.0 4545.4 571.t00003 Chromosome11 2286 99.0106 FQGEYVSNL 9 28240.4 61.4 1000000.0 1000000.0 MP03072 PFC0450w 7 CAA15614 99.0018 ILILIDAASV 10 1000000.0 88.5 1000000.0 1000000.0 MP03072 PFC0450w 19 CAA15614 99.0019 LLITFLMINL 10 1000000.0 82.3 1000000.0 1000000.0 MP03072 PFC0450w 46 CAA15614 99.0020 ALVVAIILYV 10 599232.7 38.0 1000000.0 1000000.0 MP03072 PFC0450w 50 CAA15614 99.0021 AIILYVIFLV 10 1000000.0 58.1 1000000.0 1000000.0 MP03072 PFC0450w 52 CAA15614 99.0022 ILYVIFLVLL 10 1000000.0 33.8 1000000.0 1000000.0 MP03072 PFC0450w 54 CAA15614 99.0023 YVIFLVLLFI 10 656413.8 20.3 1000000.0 1000000.0 MP03072 PFC0450w 57 CAA15614 99.0024 FLVLLFIYKA 10 139.6 80.7 498.9 1000000.0 MP03072 PFC0450w 18 CAA15614 99.0107 FLLITFLMI 9 5377.9 28.0 1000000.0 1000000.0 MP03072 PFC0450w 47 CAA15614 99.0108 LVVAIILYV 9 17753.4 20.8 1000000.0 1000000.0 MP03072 PFC0450w 50 CAA15614 99.0109 AIILYVIFL 9 35558.1 23.3 1000000.0 1000000.0 MP03072 PFC0450w 51 CAA15614 99.0110 IILYVIFLV 9 29081.2 23.4 1000000.0 1000000.0 MP03072 PFC0450w 52 CAA15614 99.0111 ILYVIFLVL 9 4626.7 49.4 1000000.0 1000000.0 MP03072 PFC0450w 55 CAA15614 99.0112 VIFLVLLFI 9 17063.1 28.6 1000000.0 1000000.0 45.t00001 Chromosome14 22 99.0113 YQDPQNYEL 9 17446.7 62.2 1000000.0 1000000.0 45.t00001 Chromosome14 134 99.0114 KTWKPTIFL 9 18939.7 82.8 1000000.0 1000000.0 45.t00001 Chromosome14 142 99.0115 LLNESNIFL 9 13381.3 66.8 1000000.0 1000000.0 45.t00001 Chromosome14 220 99.0116 FIHFFTWGT 9 54429.1 69.2 1000000.0 1000000.0 MP03137 PFC0700c 180 CAB11150 99.0117 VLFLQMMNV 9 71815.8 72.3 1000000.0 1000000.0 MP03137 PFC0700c 251 CAB11150 99.0118 NQMIFVSSI 9 39082.0 99.1 1000000.0 1000000.0 MP03137 PFC0700c 253 CAB11150 99.0119 MIFVSSIFI 9 17820.1 95.9 1000000.0 1000000.0 MP03137 PFC0700c 258 CAB11150 99.0120 SIFISFYLI 9 13357.1 72.3 1000000.0 1000000.0 MP03137 PFC0700c 293 CAB11150 99.0121 RLFEESLGI 9 22704.6 90.4 1000000.0 1000000.0 12.t00018 Chromosome14 870 99.0025 YLCLYNGLLL 10 294216.7 79.1 1000000.0 1000000.0 12.t00018 Chromosome14 1018 99.0026 YLLFFREKFL 10 1000000.0 57.8 1000000.0 1000000.0 12.t00018 Chromosome14 597 99.0122 KLIEYFLNM 9 8556.1 30.0 1000000.0 1000000.0 12.t00018 Chromosome14 615 99.0123 YVSMYIPFI 9 7367.7 57.9 1000000.0 1000000.0 12.t00018 Chromosome14 870 99.0124 YLCLYNGLL 9 12899.1 68.8 1000000.0 1000000.0 12.t00018 Chromosome14 893 99.0125 NIISSIFYI 9 94922.9 77.9 1000000.0 1000000.0 12.t00018 Chromosome14 907 99.0126 YLYDNYSHL 9 11094.9 55.2 1000000.0 1000000.0 12.t00018 Chromosome14 953 99.0127 FLNVYENFL 9 23398.0 34.3 1000000.0 1000000.0 12.t00018 Chromosome14 1037 99.0128 LIFGYNSLI 9 26493.2 50.1 1000000.0 1000000.0 12.t00018 Chromosome14 1047 99.0129 FLFYGCREV 9 24096.2 30.4 1000000.0 1000000.0 mal_BU121g9.q1c1 90 99.0130 YIYIYIYFL 9 32096.6 3.8 1000000.0 1000000.0 mal_BU121g9.q1c1 92 99.0131 YIYIYFLQI 9 15022.6 13.6 1000000.0 1000000.0 mal_9A57b11.q1t2 138 99.0132 KQYTDIPSL 9 184531.0 81.9 1000000.0 1000000.0 mal_9A57b11.q1t2 158 99.0133 KVFCYEYFI 9 10650.1 18.0 1000000.0 1000000.0 mal_9A57b11.q1t2 165 99.0134 FIFDIFKYA 9 21.1 20.2 44.0 1000000.0 mal_BL50e8.p1ca_5 6 99.0027 ALLSFLVVLV 10 1000000.0 42.5 1000000.0 1000000.0 mal_BL50e8.p1ca_5 65 99.0028 RQINFMETFV 10 1000000.0 54.6 1000000.0 1000000.0 mal_BL50e8.p1ca_5 4 99.0135 FVALLSFLV 9 3130.0 26.0 1000000.0 1000000.0 mal_BL50e8.p1ca_5 7 99.0136 LLSFLVVLV 9 11579.5 36.2 1000000.0 1000000.0 mal_BL50e8.p1ca_5 192 99.0137 FIYNWVLQT 9 30528.1 55.9 1000000.0 1000000.0 mal_BL50e8.p1ca_5 349 99.0138 ILIRALLSL 9 8963.2 44.4 1000000.0 1000000.0 mal_BL50e8.p1ca_5 353 99.0139 ALLSLDFSL 9 22110.4 36.6 1000000.0 1000000.0 mal_BL50e8.p1ca_5 562 99.0140 NLFGGGFYI 9 22065.3 23.4 1000000.0 1000000.0 mal_BL50e8.p1ca_5 779 99.0141 LMLKADYFI 9 22456.0 21.9 1000000.0 444.0 mal_BL50e8.p1ca_5 973 99.0142 NIYTHSVYV 9 245555.5 53.7 1000000.0 1000000.0 M13S8h6.p1t_3 7 99.0143 FVLACVLLI 9 10293.7 14.2 1000000.0 1000000.0 M13S8h6.p1t_3 23 99.0144 ATSTFFFFL 9 3703.8 20.0 1000000.0 1000000.0 M13S8h6.p1t_3 34 99.0145 FLLICGFCI 9 23058.3 21.3 1000000.0 1000000.0 M13S8h6.p1t_3 55 99.0146 VLITYSFTV 9 35516.3 7.8 1000000.0 1000000.0 M13S8h6.p1t_3 61 99.0147 FTVSYIFFM 9 18627.5 9.0 1000000.0 1000000.0 M13S8h6.p1t_3 77 99.0148 LLVCISILL 9 4378.4 24.2 1000000.0 1000000.0 M13S8h6.p1t_3 1447 99.0149 FIITYIWII 9 50315.1 20.9 1000000.0 1000000.0 M13S8h6.p1t_3 1469 99.0150 KMMWTIFIL 9 13621.2 14.7 1000000.0 35.6 M13S8h6.p1t_3 1538 99.0151 FVFFYIFLI 9 5681.7 3.2 1000000.0 1000000.0 M13S8h6.p1t_3 1582 99.0152 YLDRIQFLV 9 3212.4 6.0 1000000.0 1000000.0 585.t00002 Chromosome11 651 99.0029 VLSPFSLIFV 10 236320.1 33.8 1000000.0 1000000.0 585.t00002 Chromosome11 1380 99.0030 TLVNILILFL 10 1000000.0 25.5 1000000.0 1000000.0 585.t00002 Chromosome11 1406 99.0031 FVFFRFLFFV 10 132657.2 16.7 1000000.0 1000000.0 585.t00002 Chromosome11 6 99.0153 FILFYFYVM 9 18702.2 16.8 1000000.0 1000000.0 585.t00002 Chromosome11 17 99.0154 YTFCFLPVL 9 3159.4 24.6 1000000.0 1000000.0 585.t00002 Chromosome11 643 99.0155 WLFFFDLVV 9 13858.2 39.1 1000000.0 1000000.0 585.t00002 Chromosome11 661 99.0156 HLFFCIFFI 9 13336.6 6.4 1000000.0 1000000.0 585.t00002 Chromosome11 1386 99.0157 ILFLICYSI 9 18185.7 17.8 1000000.0 1000000.0 585.t00002 Chromosome11 1399 99.0158 YMFSYIPFV 9 20964.1 1.1 1000000.0 1000000.0 585.t00002 Chromosome11 1507 99.0159 YILFILFFI 9 12765.9 4.2 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1387 99.0032 LIHDDVLLFL 10 1000000.0 32.2 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 270 99.0160 FVSFYKFEV 9 10792.4 28.2 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 811 99.0161 MLWCSMESV 9 5755.3 27.5 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 924 99.0162 KLFDAINYL 9 35603.1 20.5 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1648 99.0163 FVMDITDSI 9 4215.8 44.1 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1853 99.0164 MLYSIVWGL 9 18338.7 24.8 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2301 99.0165 NIYFSYFYV 9 68948.8 41.1 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2548 99.0166 FILEHVNSI 9 80628.8 42.2 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 3057 99.0167 SLLKAQLFV 9 12372.4 15.7 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 4419 99.0168 SLDEVVLYT 9 8137.8 46.3 1000000.0 1000000.0 599.t00001 Chromosome11 1069 99.0033 HLMHIINVFI 10 1000000.0 56.9 1000000.0 1000000.0 599.t00001 Chromosome11 1341 99.0034 FLSDYTTCSV 10 93945.4 72.2 1000000.0 1000000.0 599.t00001 Chromosome11 1458 99.0035 FLRNYVVIFI 10 615882.5 83.6 1000000.0 1000000.0 599.t00001 Chromosome11 9 99.0169 YLTINFFIL 9 4373.8 64.1 1000000.0 1000000.0 599.t00001 Chromosome11 883 99.0170 NMNDIENFV 9 32886.3 78.0 1000000.0 1000000.0 599.t00001 Chromosome11 1013 99.0171 FIHDILLDL 9 11903.4 46.8 1000000.0 1000000.0 599.t00001 Chromosome11 1034 99.0172 NQYAYDLKI 9 38604.8 81.2 1000000.0 1000000.0 599.t00001 Chromosome11 1718 99.0173 GLGGLLFII 9 5216.8 74.2 1000000.0 1000000.0 599.t00001 Chromosome11 1770 99.0174 YIMNNTIFT 9 4444.5 75.2 1000000.0 1000000.0 599.t00001 Chromosome11 1914 99.0175 HLFNFSNFV 9 16629.7 25.5 1000000.0 1000000.0 MP01072 M1045c5.p1c.C_6 1138 99.0036 YLIRNILMSI 10 819635.3 75.5 1000000.0 1000000.0 MP01072 M1045c5.p1c.C_6 66 99.0176 YLYKSIFKA 9 6.2 29.5 1755.3 1000000.0 MP01072 M1045c5.p1c.C_6 82 99.0177 YLDFYEFCV 9 5138.7 6.7 1000000.0 1000000.0 MP01072 M1045c5.p1c.C_6 1161 99.0178 KIFFLFFSI 9 19713.1 22.7 1000000.0 1000000.0 MP01072 M1045c5.p1c.C_6 1281 99.0179 KLNEINILL 9 15599.8 69.4 1000000.0 1000000.0 PIR2 T28161 577 99.0037 FLMFWVAHML 10 60152.9 33.4 1000000.0 1000000.0 PIR2 T28161 142 99.0180 LLAEVCYAA 9 9.8 35.1 4774.0 1000000.0 PIR2 T28161 369 99.0181 CLYVCDPYV 9 78244.5 58.0 1000000.0 1000000.0 PIR2 T28161 577 99.0182 FLMFWVAHM 9 3061.0 5.7 1000000.0 1000000.0 PIR2 T28161 642 99.0183 FQGWGHYFV 9 53546.0 13.8 1000000.0 1000000.0 PIR2 T28161 888 99.0184 FLGDVLFAA 9 6.7 8.3 2549.7 1000000.0 PIR2 T28161 892 99.0185 VLFAANYEA 9 25.8 20.9 100.0 1000000.0 PIR2 T28161 1098 99.0186 YLQAQTTAA 9 26.9 64.0 17290.2 1000000.0 PIR2 T28161 1461 99.0187 FLRQMFYTL 9 8779.8 60.8 1000000.0 1000000.0 PIR2 T28161 2149 99.0188 FAAFTYFYL 9 11639.0 45.5 1000000.0 1000000.0 55.t00004 Chromosome14 1358 99.0038 FMDSQNGMYI 10 26503.4 87.2 1000000.0 4109.6 55.t00004 Chromosome14 1542 99.0039 SLINYNKYFV 10 1000000.0 43.5 1000000.0 1000000.0 55.t00004 Chromosome14 84 99.0189 FVVAQLYEL 9 27995.5 19.7 1000000.0 1000000.0 55.t00004 Chromosome14 480 99.0190 KTFFFFSNV 9 10931.8 72.4 1000000.0 1000000.0 55.t00004 Chromosome14 1098 99.0191 IINSDDYFV 9 58940.8 86.9 1000000.0 1000000.0 55.t00004 Chromosome14 1364 99.0192 GMYILPQYV 9 18255.9 74.7 1000000.0 1000000.0 674.t00001 Chromosome11 89 99.0040 ELVEFIFLLL 10 1000000.0 97.4 1000000.0 1000000.0 674.t00001 Chromosome11 281 99.0041 FLYKDVLMDI 10 358012.1 50.4 1000000.0 1000000.0 674.t00001 Chromosome11 89 99.0193 ELVEFIFLL 9 21772.0 47.1 1000000.0 1000000.0 674.t00001 Chromosome11 1102 99.0194 YLNKANPNI 9 12319.8 91.3 1000000.0 1000000.0 674.t00001 Chromosome11 1353 99.0195 FLQYRIPHM 9 33178.8 81.0 1000000.0 1000000.0 674.t00001 Chromosome11 1430 99.0196 YIVDIFCKI 9 11720.4 48.5 1000000.0 1000000.0

TABLE 5 Pf-derived A3,11 supertype peptides scoring positive on PIC algorithm PIC Accession Peptide A*0201 A*1101 Malaria locus Addn Source info Position No. No. Sequence AA A*0101 PIC PIC A*2402 331.t00003 Chromosome10 354 99.0197 KFEPFIIHVK 10 1000000.0 1000000.0 26.5 1000000.0 331.t00003 Chromosome10 5 99.0294 KTMDTFYKK 9 2654.1 1000000.0 0.4 1000000.0 331.t00003 Chromosome10 208 99.0295 SFFDVSKKK 9 130857.6 1000000.0 16.4 1000000.0 331.t00003 Chromosome10 435 99.0296 LSQLVHFYK 9 29656.2 1000000.0 0.6 1000000.0 331.t00003 Chromosome10 779 99.0297 SVFVRRYIK 9 18991.0 1000000.0 0.7 1000000.0 331.t00003 Chromosome10 988 99.0298 FTFQNMYVR 9 5834.2 1000000.0 22.0 1000000.0 331.t00003 Chromosome10 1324 99.0299 SQNSNTFLK 9 10099.5 1000000.0 0.4 1000000.0 331.t00003 Chromosome10 1337 99.0300 ILFHKFLNK 9 3064.6 1000000.0 2.4 1000000.0 331.t00003 Chromosome10 1521 99.0301 NLFDENFCR 9 30418.9 1000000.0 165.9 1000000.0 331.t00003 Chromosome10 1551 99.0302 ALYEKVHGK 9 9346.6 1000000.0 4.4 1000000.0 18.000811 Chr12Contig18 17 99.0198 FLLYILFLVK 10 1000000.0 1000000.0 82.1 1000000.0 18.000811 Chr12Contig18 43 99.0199 LVFSNVLCFR 10 365585.5 1000000.0 14.5 1000000.0 18.000811 Chr12Contig18 80 99.0200 AFLESQSMNK 10 1000000.0 1000000.0 65.8 1000000.0 18.000811 Chr12Contig18 112 99.0201 TFLESSFDIK 10 1000000.0 1000000.0 323.9 1000000.0 18.000811 Chr12Contig18 116 99.0202 SSFDIKSEVK 10 1000000.0 1000000.0 34.1 1000000.0 18.000811 Chr12Contig18 18 99.0303 LLYILFLVK 9 5498.6 1000000.0 10.1 1000000.0 18.000811 Chr12Contig18 129 99.0304 KSMLKELIK 9 5942.8 1000000.0 12.7 1000000.0 18.000811 Chr12Contig18 166 99.0305 PVLTSLFNK 9 10202.9 1000000.0 10.1 1000000.0 MY924Fe3.p1t1 1262 99.0203 TFICYYVMDK 10 1000000.0 1000000.0 23.0 1000000.0 MY924Fe3.p1t1 155 99.0306 NVFNIFFEK 9 10371.8 1000000.0 0.2 1000000.0 MY924Fe3.p1t1 220 99.0307 SSFLYAFNK 9 12434.3 1000000.0 0.1 1000000.0 MY924Fe3.p1t1 1030 99.0308 MFHIIMYTK 9 208352.1 1000000.0 18.2 1000000.0 MY924Fe3.p1t1 1181 99.0309 SLDDIYKYK 9 22644.9 1000000.0 2.9 1000000.0 MY924Fe3.p1t1 1613 99.0310 KVVVKNLYK 9 34654.1 1000000.0 0.9 1000000.0 MY924Fe3.p1t1 1853 99.0311 SLFRLGFVK 9 10283.0 1000000.0 0.2 1000000.0 MY924Fe3.p1t1 2012 99.0312 SLFFNSLYY 9 4.6 1000000.0 2.6 1000000.0 MY924Fe3.p1t1 2238 99.0313 ITFEKNYYR 9 21591.6 1000000.0 1.5 1000000.0 MY924Fe3.p1t1 2285 99.0314 SQYEENKSK 9 139775.3 1000000.0 39.1 1000000.0 MP03001 MAL3P2.11 57 CAB38998 99.0204 KQENWYSLKK 10 1000000.0 1000000.0 50.6 1000000.0 MP03001 MAL3P2.11 335 CAB38998 99.0205 VTCGNGIQVR 10 1000000.0 1000000.0 170.6 1000000.0 MP03001 MAL3P2.11 17 CAB38998 99.0315 ALFQEYQCY 9 3.4 1000000.0 72.7 1000000.0 MP03001 MAL3P2.11 57 CAB38998 99.0316 KQENWYSLK 9 44996.2 1000000.0 173.7 1000000.0 1369.t00001 Chromosome11 44 99.0206 TLYQIQVMKR 10 1000000.0 1000000.0 52.0 1000000.0 1369.t00001 Chromosome11 58 99.0207 KQVQMMIMIK 10 1000000.0 1000000.0 8.7 1000000.0 1369.t00001 Chromosome11 70 99.0208 GVIYIMIISK 10 1000000.0 1000000.0 10.6 1000000.0 1369.t00001 Chromosome11 158 99.0209 ELFDKDTFFK 10 1000000.0 1000000.0 14.2 1000000.0 1369.t00001 Chromosome11 18 99.0317 KTMNNYMIK 9 16730.1 1000000.0 1.1 1000000.0 1369.t00001 Chromosome11 159 99.0318 LFDKDTFFK 9 32977.1 1000000.0 126.3 1000000.0 1369.t00001 Chromosome11 287 99.0319 YLFNQHIKK 9 21347.4 1000000.0 8.2 1000000.0 1369.t00001 Chromosome11 307 99.0320 MQSSFFMNR 9 12685.3 1000000.0 25.4 1000000.0 1369.t00001 Chromosome11 315 99.0321 RFYITTRYK 9 258367.4 1000000.0 21.4 1000000.0 1369.t00001 Chromosome11 319 99.0322 TTRYKYLNK 9 10429.2 1000000.0 4.5 1000000.0 699.t00001 Chromosome11 464 99.0210 KVCELLGYYK 10 1000000.0 1000000.0 1.1 1000000.0 699.t00001 Chromosome11 492 99.0211 SFLLLIVFSK 10 1000000.0 1000000.0 21.9 1000000.0 699.t00001 Chromosome11 623 99.0212 KLLYKMNYLK 10 1000000.0 1000000.0 15.0 1000000.0 699.t00001 Chromosome11 764 99.0213 TLEYNPSFFY 10 91.9 1000000.0 219.0 1000000.0 699.t00001 Chromosome11 782 99.0214 LLYNHITSIK 10 1000000.0 1000000.0 12.1 1000000.0 699.t00001 Chromosome11 878 99.0215 LFYLYMNFLK 10 1000000.0 1000000.0 8.2 1000000.0 699.t00001 Chromosome11 386 99.0323 KQNIPIYIY 9 57.8 1000000.0 175.4 1000000.0 699.t00001 Chromosome11 507 99.0324 KTNIFFKKK 9 23058.6 1000000.0 1.5 1000000.0 699.t00001 Chromosome11 734 99.0325 IVNDLGIFY 9 2.4 1000000.0 16.6 1000000.0 699.t00001 Chromosome11 769 99.0326 PSFFYLSFK 9 22074.6 1000000.0 20.1 1000000.0 mal_4T2c4.p1t1 15 99.0216 ILLIRPMLVK 10 1000000.0 1000000.0 95.1 1000000.0 mal_4T2c4.p1t1 29 99.0217 LVKLRPMLVK 10 1000000.0 1000000.0 22.3 1000000.0 mal_4T2c4.p1t1 36 99.0218 LVKLGPILVK 10 1000000.0 1000000.0 15.0 1000000.0 mal_4T2c4.p1t1 16 99.0327 LLIRPMLVK 9 29115.0 1000000.0 16.1 1000000.0 M13Hg2.q1t3 97 99.0219 LLSRFIFIYK 10 1000000.0 1000000.0 12.9 1000000.0 M13Hg2.q1t3 267 99.0220 KTSDAKLVDK 10 543207.5 1000000.0 21.8 1000000.0 M13Hg2.q1t3 277 99.0221 ETSTISTFIK 10 714638.7 1000000.0 21.8 1000000.0 M13Hg2.q1t3 406 99.0222 IFFSYNPFHK 10 1000000.0 1000000.0 18.5 1000000.0 M13Hg2.q1t3 528 99.0223 YFFNCIQMAK 10 1000000.0 1000000.0 48.6 1000000.0 M13Hg2.q1t3 9 99.0328 SLYNKIEYR 9 32837.9 1000000.0 36.8 1000000.0 M13Hg2.q1t3 48 99.0329 SASESNFYK 9 17208.3 1000000.0 0.2 1000000.0 M13Hg2.q1t3 216 99.0330 ISYIFPLFK 9 12671.6 1000000.0 2.2 1000000.0 M13Hg2.q1t3 420 99.0331 SQNYENINK 9 36248.0 1000000.0 3.6 1000000.0 M13Hg2.q1t3 661 99.0332 SLMDASKNK 9 5327.4 1000000.0 3.2 1000000.0 Mal_5L10c4.q1t6 21 99.0333 KLGFFVCYK 9 42997.2 1000000.0 3.5 1000000.0 Mal_5L10c4.q1t6 36 99.0334 SFKNKILQK 9 139254.7 1000000.0 14.9 1000000.0 Mal_5L10c4.q1t6 56 99.0335 KFMYLRKKK 9 74875.0 1000000.0 33.4 1000000.0 Mal_5L10c4.q1t6 381 99.0336 KQIIFEALK 9 120283.5 1000000.0 38.9 1000000.0 Mal_5L10c4.q1t6 519 99.0337 ETFYKELYK 9 14646.9 1000000.0 1.2 1000000.0 Mal_5L10c4.q1t6 537 99.0338 SVNYFLLER 9 4574.8 1000000.0 0.4 1000000.0 Mal_5L10c4.q1t6 724 99.0339 ILNFLNFNK 9 12039.7 1000000.0 2.7 1000000.0 Mal_5L10c4.q1t6 897 99.0340 NTCSKEIYK 9 26259.6 1000000.0 4.6 1000000.0 Mal_5L10c4.q1t6 1316 99.0341 KLRNFLFYY 9 34.8 1000000.0 27.7 1000000.0 Mal_5L10c4.q1t6 1722 99.0342 CSNNNIFYK 9 16887.2 1000000.0 2.7 1000000.0 571.t00003 Chromosome11 1059 99.0224 MQYNHDNIYK 10 1000000.0 1000000.0 6.8 1000000.0 571.t00003 Chromosome11 2438 99.0225 SFSMLYLFGK 10 1000000.0 1000000.0 20.1 1000000.0 571.t00003 Chromosome11 675 99.0343 ALNPKYQNH 9 4302.1 1000000.0 149.6 1000000.0 571.t00003 Chromosome11 749 99.0344 TLNSFQHNK 9 9140.5 1000000.0 4.0 1000000.0 571.t00003 Chromosome11 1220 99.0345 KINEFQWEK 9 55899.8 1000000.0 0.3 1000000.0 571.t00003 Chromosome11 1368 99.0346 RSDYFHNTK 9 15625.8 1000000.0 5.2 1000000.0 571.t00003 Chromosome11 1429 99.0347 STNSQQLIK 9 14992.1 1000000.0 1.1 1000000.0 571.t00003 Chromosome11 1552 99.0348 KFMTPTTLK 9 54389.6 1000000.0 8.1 1000000.0 571.t00003 Chromosome11 1684 99.0349 TTNSTPHFK 9 5905.8 1000000.0 3.8 1000000.0 571.t00003 Chromosome11 2509 99.0350 KLMETRFSK 9 8313.3 1000000.0 2.8 1000000.0 MP03072 PFC0450w 36 CAA15614 99.0226 SQAHRENGKK 10 1000000.0 1000000.0 109.2 1000000.0 MP03072 PFC0450w 45 CAA15614 99.0227 KALVVAIILY 10 220.1 1000000.0 237.1 1000000.0 MP03072 PFC0450w 55 CAA15614 99.0228 VIFLVLLFIY 10 137.2 1000000.0 61.8 1000000.0 MP03072 PFC0450w 56 CAA15614 99.0229 IFLVLLFIYK 10 1000000.0 1000000.0 44.3 1000000.0 MP03072 PFC0450w 58 CAA15614 99.0230 LVLLFIYKAY 10 371.7 1000000.0 207.5 1000000.0 MP03072 PFC0450w 59 CAA15614 99.0231 VLLFIYKAYK 10 1000000.0 1000000.0 31.2 1000000.0 MP03072 PFC0450w 61 CAA15614 99.0232 LFIYKAYKNK 10 1000000.0 1000000.0 434.4 1000000.0 MP03072 PFC0450w 72 CAA15614 99.0233 KLYTNFFMKK 10 1000000.0 1000000.0 5.8 1000000.0 MP03072 PFC0450w 92 CAA15614 99.0234 STYLSASDEY 10 57.2 1000000.0 85.1 1000000.0 MP03072 PFC0450w 36 CAA15614 99.0351 SQAHRENGK 9 65339.9 1000000.0 230.0 1000000.0 MP03072 PFC0450w 46 CAA15614 99.0352 ALVVAIILY 9 6.0 1000000.0 95.4 1000000.0 MP03072 PFC0450w 57 CAA15614 99.0353 FLVLLFIYK 9 14940.5 1000000.0 5.0 1000000.0 MP03072 PFC0450w 58 CAA15614 99.0354 LVLLFIYKA 9 13.1 102.2 132.5 1000000.0 MP03072 PFC0450w 60 CAA15614 99.0355 LLFIYKAYK 9 59055.3 1000000.0 9.6 1000000.0 MP03072 PFC0450w 62 CAA15614 99.0356 FIYKAYKNK 9 35013.8 1000000.0 22.0 1000000.0 MP03072 PFC0450w 72 CAA15614 99.0357 KLYTNFFMK 9 7491.5 1000000.0 2.3 1000000.0 MP03072 PFC0450w 74 CAA15614 99.0358 YTNFFMKKR 9 18478.3 1000000.0 48.4 1000000.0 45.t00001 Chromosome14 50 99.0235 ALERLLSLKK 10 1000000.0 1000000.0 149.5 1000000.0 45.t00001 Chromosome14 109 99.0236 KILIKIPVTK 10 1000000.0 1000000.0 30.2 1000000.0 45.t00001 Chromosome14 128 99.0237 RLPLLPKTWK 10 1000000.0 1000000.0 19.6 1000000.0 45.t00001 Chromosome14 147 99.0238 NIFLRFIPDK 10 1000000.0 1000000.0 24.9 1000000.0 45.t00001 Chromosome14 161 99.0239 SQVSNSDSYK 10 1000000.0 1000000.0 36.0 1000000.0 45.t00001 Chromosome14 197 99.0240 QQNQESKIMK 10 928526.9 1000000.0 431.5 1000000.0 45.t00001 Chromosome14 249 99.0241 IIALLIIPPK 10 1000000.0 1000000.0 19.3 1000000.0 45.t00001 Chromosome14 374 99.0242 SQDLACIFDA 10 226.7 389.1 400.3 1000000.0 45.t00001 Chromosome14 34 99.0359 AVIFTPIYY 9 7.6 1000000.0 4.7 1000000.0 45.t00001 Chromosome14 50 99.0360 ALERLLSLK 9 6245.7 1000000.0 55.5 1000000.0 45.t00001 Chromosome14 85 99.0361 SISGKYDIK 9 29562.3 1000000.0 25.1 1000000.0 45.t00001 Chromosome14 101 99.0362 ILCIEGEQK 9 51943.1 1000000.0 162.5 1000000.0 45.t00001 Chromosome14 126 99.0363 EQRLPLLPK 9 66848.0 1000000.0 244.3 1000000.0 45.t00001 Chromosome14 148 99.0364 IFLRFIPDK 9 170326.8 1000000.0 112.0 1000000.0 45.t00001 Chromosome14 250 99.0365 IALLIIPPK 9 47443.5 1000000.0 25.2 1000000.0 45.t00001 Chromosome14 270 99.0366 PVVCSMEYK 9 20870.3 1000000.0 23.1 1000000.0 45.t00001 Chromosome14 271 99.0367 VVCSMEYKK 9 24792.5 1000000.0 8.3 1000000.0 45.t00001 Chromosome14 308 99.0368 FSYDLRLNK 9 5228.9 1000000.0 13.4 1000000.0 45.t00001 Chromosome14 323 99.0369 HLNIPIGFK 9 25082.0 1000000.0 98.3 1000000.0 MP03137 PFC0700c 14 CAB11150 99.0243 SSPLFNNFYK 10 1000000.0 1000000.0 0.5 1000000.0 MP03137 PFC0700c 151 CAB11150 99.0244 FLYLLNKKNK 10 1000000.0 1000000.0 139.2 1000000.0 MP03137 PFC0700c 183 CAB11150 99.0245 LQMMNVNLQK 10 1000000.0 1000000.0 83.6 1000000.0 MP03137 PFC0700c 195 CAB11150 99.0246 LTNHLINTPK 10 427675.0 1000000.0 20.8 1000000.0 MP03137 PFC0700c 259 CAB11150 99.0247 IFISFYLINK 10 1000000.0 1000000.0 102.0 1000000.0 MP03137 PFC0700c 293 CAB11150 99.0248 RLFEESLGIR 10 923199.1 1000000.0 420.0 1000000.0 MP03137 PFC0700c 16 CAB11150 99.0370 PLFNNFYKR 9 11760.5 1000000.0 383.0 1000000.0 MP03137 PFC0700c 141 CAB11150 99.0371 YQNFQNADK 9 40121.5 1000000.0 637.4 1000000.0 MP03137 PFC0700c 184 CAB11150 99.0372 QMMNVNLQK 9 17662.1 1000000.0 1.4 1000000.0 MP03137 PFC0700c 222 CAB11150 99.0373 AVSEIQNNK 9 6991.0 1000000.0 3.1 1000000.0 MP03137 PFC0700c 236 CAB11150 99.0374 GTMYILLKK 9 986.2 1000000.0 0.5 1000000.0 MP03137 PFC0700c 260 CAB11150 99.0375 FISFYLINK 9 7376.0 1000000.0 12.2 1000000.0 MP03137 PFC0700c 264 CAB11150 99.0376 YLINKHWQR 9 39562.3 1000000.0 41.6 1000000.0 MP03137 PFC0700c 273 CAB11150 99.0377 ALKISQLQK 9 37884.8 1000000.0 5.1 1000000.0 MP03137 PFC0700c 282 CAB11150 99.0378 KINSNFLLK 9 5732.3 1000000.0 1.0 1000000.0 12.t00018 Chromosome14 89 99.0249 QLKHFFNSNK 10 1000000.0 1000000.0 33.5 1000000.0 12.t00018 Chromosome14 615 99.0250 YVSMYIPFIK 10 301060.0 1000000.0 2.6 1000000.0 12.t00018 Chromosome14 671 99.0251 VLFYIYNMYH 10 900700.0 1000000.0 13.6 1000000.0 12.t00018 Chromosome14 705 99.0252 YTYIFFNYDK 10 742244.6 1000000.0 2.1 1000000.0 12.t00018 Chromosome14 1140 99.0253 SFFITYSYWK 10 1000000.0 1000000.0 5.7 1000000.0 12.t00018 Chromosome14 195 99.0379 STSNKHINR 9 6609.8 1000000.0 3.8 1000000.0 12.t00018 Chromosome14 687 99.0380 SQCNDYYIK 9 95255.3 1000000.0 6.3 1000000.0 12.t00018 Chromosome14 896 99.0381 SSIFYIKNK 9 41588.5 1000000.0 8.4 1000000.0 12.t00018 Chromosome14 1020 99.0382 LFFREKFLK 9 89243.3 1000000.0 14.3 1000000.0 12.t00018 Chromosome14 1160 99.0383 ILDNVSFLK 9 7621.1 1000000.0 21.0 1000000.0 mal_BU121g9.q1c1 10 99.0254 ILVLDIPGFK 10 1000000.0 1000000.0 55.0 1000000.0 mal_BU121g9.q1c1 45 99.0255 ETYGDSLVLH 10 453286.5 1000000.0 386.1 1000000.0 mal_BU121g9.q1c1 59 99.0256 EVGYFKRIFK 10 1000000.0 1000000.0 20.4 1000000.0 mal_BU121g9.q1c1 11 99.0384 LVLDIPGFK 9 13172.2 1000000.0 26.7 1000000.0 mal_BU121g9.q1c1 30 99.0385 GMLTVAGPR 9 54761.5 1000000.0 326.1 1000000.0 mal_BU121g9.q1c1 39 99.0386 SQTELFETY 9 6.7 1000000.0 254.2 1000000.0 mal_BU121g9.q1c1 48 99.0387 GDSLVLHAK 9 19504.9 1000000.0 306.8 1000000.0 mal_BU121g9.q1c1 50 99.0388 SLVLHAKER 9 133501.5 1000000.0 487.4 1000000.0 mal_BU121g9.q1c1 60 99.0389 VGYFKRIFK 9 44416.3 1000000.0 27.9 1000000.0 mal_BU121g9.q1c1 86 99.0390 NIYIYIYIY 9 40.2 1000000.0 322.7 1000000.0 mal_BU121g9.q1c1 88 99.0391 YIYIYIYIY 9 16.2 1000000.0 310.0 1000000.0 mal_9A57b11.q1t2 31 99.0257 SSFNCDIANK 10 1000000.0 1000000.0 8.4 1000000.0 mal_9A57b11.q1t2 49 99.0258 SMGVFCLKEK 10 1000000.0 1000000.0 24.6 1000000.0 mal_9A57b11.q1t2 119 99.0259 HIVKNRIYNK 10 1000000.0 1000000.0 51.7 1000000.0 mal_9A57b11.q1t2 128 99.0260 KLKLHKIIRK 10 1000000.0 1000000.0 64.9 1000000.0 mal_9A57b11.q1t2 165 99.0261 FIFDIFKYAR 10 1000000.0 1000000.0 148.8 1000000.0 mal_9A57b11.q1t2 202 99.0262 AQKALSNLHK 10 1000000.0 1000000.0 113.8 1000000.0 mal_9A57b11.q1t2 208 99.0263 NLHKSWLQYK 10 507559.4 1000000.0 199.6 1000000.0 mal_9A57b11.q1t2 234 99.0264 YLPLFLMMEH 10 1000000.0 1000000.0 147.3 1000000.0 mal_9A57b11.q1t2 32 99.0392 SFNCDIANK 9 27329.1 1000000.0 35.4 1000000.0 mal_9A57b11.q1t2 62 99.0393 KINKKYNKK 9 40379.4 1000000.0 56.4 1000000.0 mal_9A57b11.q1t2 95 99.0394 ILNNKELFK 9 13663.7 1000000.0 29.6 1000000.0 mal_9A57b11.q1t2 120 99.0395 IVKNRIYNK 9 25949.5 1000000.0 17.8 1000000.0 mal_9A57b11.q1t2 154 99.0396 LINSKVFCY 9 6.1 1000000.0 113.8 1000000.0 mal_9A57b11.q1t2 183 99.0397 RQKEFYPIK 9 127059.4 1000000.0 38.7 1000000.0 mal_BL50e8.p1ca_5 9 99.0265 SFLVVLVFNK 10 1000000.0 1000000.0 33.6 1000000.0 mal_BL50e8.p1ca_5 152 99.0266 STYMTPSAIK 10 1000000.0 1000000.0 2.8 1000000.0 mal_BL50e8.p1ca_5 656 99.0267 KLYGEFTMNK 10 1000000.0 1000000.0 1.3 1000000.0 mal_BL50e8.p1ca_5 907 99.0268 GVYYIFVYLR 10 1000000.0 1000000.0 3.7 1000000.0 mal_BL50e8.p1ca_5 115 99.0398 SQYSNYFDY 9 11.0 1000000.0 15.2 1000000.0 mal_BL50e8.p1ca_5 361 99.0399 LFITYFQQK 9 90294.9 1000000.0 50.9 1000000.0 mal_BL50e8.p1ca_5 409 99.0400 ATSWDEYPK 9 44148.4 1000000.0 0.8 1000000.0 mal_BL50e8.p1ca_5 752 99.0401 ASFAAHENK 9 11256.9 1000000.0 0.2 1000000.0 mal_BL50e8.p1ca_5 780 99.0402 MLKADYFIR 9 35925.9 1000000.0 61.1 1000000.0 mal_BL50e8.p1ca_5 819 99.0403 VLNPVTIPK 9 14931.7 1000000.0 5.6 1000000.0 M13S8h6.p1t_3 63 99.0269 VSYIFFMSFK 10 1000000.0 1000000.0 0.4 1000000.0 M13S8h6.p1t_3 937 99.0270 MQKYFLHISK 10 1000000.0 1000000.0 37.5 1000000.0 M13S8h6.p1t_3 25 99.0404 STFFFFLSR 9 3848.4 1000000.0 0.1 1000000.0 M13S8h6.p1t_3 84 99.0405 LLLTFGVYY 9 22.7 1000000.0 157.5 1000000.0 M13S8h6.p1t_3 157 99.0406 KFLFRYKQK 9 941796.8 1000000.0 16.1 1000000.0 M13S8h6.p1t_3 394 99.0407 KVFIKGKGK 9 43309.1 1000000.0 3.8 1000000.0 M13S8h6.p1t_3 1449 99.0408 ITYIWIILK 9 6990.4 1000000.0 1.6 1000000.0 M13S8h6.p1t_3 1534 99.0409 KFFFFVFFY 9 51.8 1000000.0 3.5 2.2 M13S8h6.p1t_3 1655 99.0410 KLLQKLISK 9 8661.9 1000000.0 53.4 1000000.0 M13S8h6.p1t_3 1703 99.0411 ILNILKLAK 9 21447.1 1000000.0 55.0 1000000.0 585.t00002 Chromosome11 193 99.0412 SQNNFSKIK 9 90378.2 1000000.0 9.1 1000000.0 585.t00002 Chromosome11 300 99.0413 SSLNIYNTK 9 46908.8 1000000.0 5.2 1000000.0 585.t00002 Chromosome11 529 99.0414 KLFNYKFFK 9 60297.3 1000000.0 1.0 1000000.0 585.t00002 Chromosome11 572 99.0415 LTFLSNIRK 9 13099.9 1000000.0 1.3 1000000.0 585.t00002 Chromosome11 616 99.0416 KFFYIFHYK 9 49030.6 1000000.0 0.2 1000000.0 585.t00002 Chromosome11 1415 99.0417 VTCSYFIIR 9 6831.4 1000000.0 16.8 1000000.0 585.t00002 Chromosome11 1487 99.0418 LTCAFKIYK 9 25752.8 1000000.0 0.3 1000000.0 585.t00002 Chromosome11 1508 99.0419 ILFILFFIK 9 9492.2 1000000.0 1.2 1000000.0 585.t00002 Chromosome11 1541 99.0420 NLYFFIHNR 9 13239.8 1000000.0 59.3 1000000.0 585.t00002 Chromosome11 1742 99.0421 IFLHYYFKK 9 118461.5 1000000.0 7.6 1000000.0 1223.t00015 mal_9A21f9.q1t_4 4294 99.0271 QVFFLQEMER 10 544655.4 1000000.0 27.6 1000000.0 1223.t00015 mal_9A21f9.q1t_4 272 99.0422 SFYKFEVEK 9 193104.9 1000000.0 16.1 1000000.0 1223.t00015 mal_9A21f9.q1t_4 325 99.0423 KTFREHFLK 9 17344.2 1000000.0 0.022 1000000.0 1223.t00015 mal_9A21f9.q1t_4 992 99.0424 VSNSSQLFK 9 13528.2 1000000.0 5.1 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1397 99.0425 SLLNDVFPK 9 67376.3 1000000.0 1.2 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1627 99.0426 KLFIFYLDK 9 25288.3 1000000.0 0.67 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1664 99.0427 LLNSQIIQY 9 18.6 1000000.0 160.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2115 99.0428 FQGFYFLDK 9 6204.2 1000000.0 44.3 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2412 99.0429 NTFSFSWMK 9 16414.9 1000000.0 0.20 1000000.0 1223.t00015 mal_9A21f9.q1t_4 4500 99.0430 MFYNCPVYK 9 327575.1 1000000.0 10.3 1000000.0 599.t00001 Chromosome11 723 99.0272 NLLRHAIFYK 10 1000000.0 1000000.0 7.4 1000000.0 599.t00001 Chromosome11 1288 99.0273 SSYGYNIYFK 10 1000000.0 1000000.0 0.3 1000000.0 599.t00001 Chromosome11 1451 99.0274 RTYVNEYFLR 10 1000000.0 1000000.0 25.4 1000000.0 599.t00001 Chromosome11 16 99.0431 ILLTLVFQK 9 46527.3 1000000.0 2.9 1000000.0 599.t00001 Chromosome11 28 99.0432 CQNSLNYSK 9 38238.7 1000000.0 63.2 1000000.0 599.t00001 Chromosome11 211 99.0433 IVNNTELNK 9 9493.8 1000000.0 3.6 1000000.0 599.t00001 Chromosome11 776 99.0434 TLFSQNLFY 9 10.5 1000000.0 75.0 1000000.0 599.t00001 Chromosome11 1320 99.0435 TFYESVFTR 9 63945.9 1000000.0 27.9 1000000.0 599.t00001 Chromosome11 1370 99.0436 YFFEEFFNK 9 19717.0 1000000.0 4.6 1000000.0 599.t00001 Chromosome11 1903 99.0437 TTQSNNIYK 9 20011.8 1000000.0 2.1 1000000.0 MP01072 M1045c5.p1c.C_6 1451 99.0275 SLFYFTSNGK 10 1000000.0 1000000.0 8.0 1000000.0 MP01072 M1045c5.p1c.C_6 46 99.0438 KLNYDNFEK 9 48445.0 1000000.0 3.4 1000000.0 MP01072 M1045c5.p1c.C_6 327 99.0439 ILCDDGIYR 9 19413.7 1000000.0 65.3 1000000.0 MP01072 M1045c5.p1c.C_6 359 99.0440 KVADVFLQH 9 6428.6 1000000.0 4.4 1000000.0 MP01072 M1045c5.p1c.C_6 419 99.0441 STSFLFLRK 9 2370.1 1000000.0 0.2 1000000.0 MP01072 M1045c5.p1c.C_6 421 99.0442 SFLFLRKQK 9 408258.6 1000000.0 12.7 1000000.0 MP01072 M1045c5.p1c.C_6 558 99.0443 SFFSSCENK 9 55537.2 1000000.0 17.7 1000000.0 MP01072 M1045c5.p1c.C_6 609 99.0444 AQSSYIYNK 9 18056.8 1000000.0 2.5 1000000.0 MP01072 M1045c5.p1c.C_6 1027 99.0445 MSAKYLYHK 9 5370.6 1000000.0 8.8 1000000.0 MP01072 M1045c5.p1c.C_6 1047 99.0446 TTLFSHFNK 9 10524.0 1000000.0 0.2 1000000.0 MP01072 M1045c5.p1c.C_6 1215 99.0447 SVYYNTMLR 9 9856.9 1000000.0 1.2 1000000.0 PIR2 T28161 1124 99.0276 VVNFLFELYK 10 408697.6 1000000.0 3.5 1000000.0 PIR2 T28161 1403 99.0277 TFFLWDRYKK 10 1000000.0 1000000.0 9.0 1000000.0 PIR2 T28161 108 99.0448 SVGACAPYR 9 59804.6 1000000.0 2.1 1000000.0 PIR2 T28161 204 99.0449 KQLEDNLRK 9 87893.1 1000000.0 16.9 1000000.0 PIR2 T28161 758 99.0450 KVASNMHHK 9 6948.7 1000000.0 1.6 1000000.0 PIR2 T28161 760 99.0451 ASNMHHKKK 9 32965.2 1000000.0 4.3 1000000.0 PIR2 T28161 838 99.0452 AGFISNTYK 9 154161.8 1000000.0 2.2 1000000.0 PIR2 T28161 965 99.0453 ILAFKEIYK 9 14274.5 1000000.0 12.6 1000000.0 PIR2 T28161 1879 99.0454 ALFKRWLEY 9 3.4 1000000.0 27.4 1000000.0 PIR2 T28161 2151 99.0455 AFTYFYLKK 9 40565.6 1000000.0 1.6 1000000.0 55.t00004 Chromosome14 483 99.0278 FFFSNVNNNK 10 409139.5 1000000.0 408.4 1000000.0 55.t00004 Chromosome14 564 99.0279 SQGKKNTYLK 10 1000000.0 1000000.0 13.0 1000000.0 55.t00004 Chromosome14 976 99.0280 VFNNSIILEK 10 1000000.0 1000000.0 372.4 1000000.0 55.t00004 Chromosome14 1338 99.0281 SVSEGYTSTY 10 67.8 1000000.0 33.5 1000000.0 55.t00004 Chromosome14 229 99.0456 TSICKYWIK 9 8242.3 1000000.0 14.6 1000000.0 55.t00004 Chromosome14 263 99.0457 TTICKHWKK 9 4558.7 1000000.0 1.7 1000000.0 55.t00004 Chromosome14 537 99.0458 KVTNVHIYK 9 41321.8 1000000.0 0.2 1000000.0 55.t00004 Chromosome14 866 99.0459 ITNMNNINR 9 5371.8 1000000.0 37.6 1000000.0 55.t00004 Chromosome14 909 99.0460 MLNIYKINK 9 17179.3 1000000.0 13.6 1000000.0 55.t00004 Chromosome14 1030 99.0461 IINSYIDYK 9 84561.6 1000000.0 2.0 1000000.0 55.t00004 Chromosome14 1141 99.0462 NLYTYVVNK 9 45076.1 1000000.0 54.8 1000000.0 55.t00004 Chromosome14 1665 99.0463 KMIYSIFIK 9 42191.9 1000000.0 4.1 1000000.0 13.t00011 Chromosome14 8 99.0282 ISMDKSLFFK 10 1000000.0 1000000.0 16.7 1000000.0 13.t00011 Chromosome14 47 99.0283 TVFLDYVKGK 10 1000000.0 1000000.0 7.8 1000000.0 13.t00011 Chromosome14 59 99.0284 DVYKETNMNR 10 1000000.0 1000000.0 64.9 1000000.0 13.t00011 Chromosome14 117 99.0285 KLKKSTICNK 10 1000000.0 1000000.0 59.9 1000000.0 13.t00011 Chromosome14 9 99.0464 SMDKSLFFK 9 4208.2 1000000.0 3.5 1000000.0 13.t00011 Chromosome14 12 99.0465 KSLFFKSLK 9 64105.1 1000000.0 17.4 1000000.0 13.t00011 Chromosome14 48 99.0466 VFLDYVKGK 9 347222.4 1000000.0 216.7 1000000.0 13.t00011 Chromosome14 93 99.0467 KVKRFRVFK 9 52490.3 1000000.0 3.3 1000000.0 13.t00011 Chromosome14 104 99.0468 SFFIDEVKK 9 352606.0 1000000.0 37.8 1000000.0 13.t00011 Chromosome14 112 99.0469 KIYENKLKK 9 30696.4 1000000.0 14.5 1000000.0 37.t00002 Chromosome14 13 99.0286 ALTYMYCVYY 10 249.1 1000000.0 112.8 1000000.0 37.t00002 Chromosome14 31 99.0287 SQISIFCNLR 10 1000000.0 1000000.0 226.6 1000000.0 37.t00002 Chromosome14 32 99.0288 QISIFCNLRR 10 301919.5 1000000.0 80.8 1000000.0 37.t00002 Chromosome14 62 99.0289 VCNNETYYNK 10 1000000.0 1000000.0 186.8 1000000.0 37.t00002 Chromosome14 71 99.0290 KAHEENDKVK 10 1000000.0 1000000.0 956.7 1000000.0 37.t00002 Chromosome14 13 99.0470 ALTYMYCVY 9 9.1 1000000.0 279.6 1000000.0 37.t00002 Chromosome14 32 99.0471 QISIFCNLR 9 26897.2 1000000.0 855.0 1000000.0 37.t00002 Chromosome14 33 99.0472 ISIFCNLRR 9 37287.9 1000000.0 255.9 1000000.0 37.t00002 Chromosome14 61 99.0473 NVCNNETYY 9 25.3 1000000.0 514.8 1000000.0 674.t00001 Chromosome11 90 99.0291 LVEFIFLLLK 10 304423.1 1000000.0 13.7 1000000.0 674.t00001 Chromosome11 218 99.0292 SVFYNKEIIK 10 993500.3 1000000.0 4.5 1000000.0 674.t00001 Chromosome11 867 99.0293 SLKDFDMLLY 10 199.3 1000000.0 214.4 1000000.0 674.t00001 Chromosome11 64 99.0474 NVNDRFVEK 9 13728.8 1000000.0 11.8 1000000.0 674.t00001 Chromosome11 662 99.0475 TLSNSLPQK 9 36834.4 1000000.0 47.0 1000000.0 674.t00001 Chromosome11 673 99.0476 YQINNFIHK 9 12103.7 1000000.0 59.8 1000000.0 674.t00001 Chromosome11 689 99.0477 NLTINNFQK 9 59129.2 1000000.0 40.3 1000000.0 674.t00001 Chromosome11 1035 99.0478 KFNRDMLQK 9 254779.4 1000000.0 1.9 1000000.0 674.t00001 Chromosome11 1126 99.0479 NQSDFLLLK 9 8015.9 1000000.0 15.2 1000000.0 674.t00001 Chromosome11 1256 99.0480 SFHHFNIDK 9 178323.3 1000000.0 26.2 1000000.0 674.t00001 Chromosome11 1288 99.0481 KSKELLLQK 9 27230.7 1000000.0 4.4 1000000.0

TABLE 6 Pf-derived 15mer peptides with nonamer core sequences scoring DR1 PIC <4 nM Peptide Antigen Addn Source info Position No. Sequence AA DR1 PIC 331.t00003 Chromosome10 182 100.0001 LSHFKKNFILQNNEE 15 0.447 331.t00003 Chromosome10 365 100.0002 TTFLSALKLLKIAQY 15 0.400 331.t00003 Chromosome10 428 100.0003 NNKLSKNLSQLVHFY 15 0.130 331.t00003 Chromosome10 617 100.0004 KIYMFGGFSKGVRNN 15 0.061 331.t00003 Chromosome10 894 100.0005 DDMIGMPNLSSTVVC 15 0.337 331.t00003 Chromosome10 987 100.0006 TFTFQNMYVRSKVVS 15 0.400 331.t00003 Chromosome10 1365 100.0007 KYEIIGNILIFHYKY 15 0.435 331.t00003 Chromosome10 1601 100.0008 KERMKNMYIVSNNDD 15 0.013 331.t00003 Chromosome10 1656 100.0009 GVGYFTLPLLKCIEA 15 0.302 331.t00003 Chromosome10 1725 100.0010 HRIILGLLPHSQPAW 15 0.167 Chr12Contig18 18.000811 13 100.0011 HFFLFLLYILFLVKM 15 1.826 Chr12Contig18 18.000811 16 100.0012 LFLLYILFLVKMNAL 15 0.593 Chr12Contig18 18.000811 21 100.0013 ILFLVKMNALRRLPV 15 0.035 Chr12Contig18 18.000811 27 100.0014 MNALRRLPVICSFLV 15 3.206 Chr12Contig18 18.000811 79 100.0015 SAFLESQSMNKIGDD 15 3.392 Chr12Contig18 18.000811 132 100.0016 LKELIKVGLPSFENL 15 0.785 Chr12Contig18 18.000811 143 100.0017 FENLVAENVKPPKVD 15 0.854 Chr12Contig18 18.000811 148 100.0018 AENVKPPKVDPATYG 15 3.392 Chr12Contig18 18.000811 158 100.0019 PATYGIIVPVLTSLF 15 0.221 Chr12Contig18 18.000811 161 100.0020 YGIIVPVLTSLFNKV 15 0.956 MY924Fe3.p1t1 1015 100.0021 SVDLQIKISMKVLNS 15 0.103 MY924Fe3.p1t1 1021 100.0022 KISMKVLNSMFHIIM 15 0.234 MY924Fe3.p1t1 1076 100.0023 KDVVQIQTVLLSLGF 15 0.066 MY924Fe3.p1t1 1331 100.0024 SQIIIILPSILENIL 15 0.092 MY924Fe3.p1t1 1526 100.0025 MHSVKEMIVYLIQNN 15 0.262 MY924Fe3.p1t1 1703 100.0026 TINLINELMKRQHDK 15 0.192 MY924Fe3.p1t1 1746 100.0027 REMLLKMKSMSRNQR 15 0.130 MY924Fe3.p1t1 1878 100.0028 RSIIFAGHTIELNSL 15 0.248 MY924Fe3.p1t1 1890 100.0029 NSLMFKQTSGRAGRR 15 0.061 MY924Fe3.p1t1 2201 100.0030 NLIITYLLIKKVLHN 15 0.162 MP03001 MAL3P2.11 1 100.0031 MRKLAILSVSSFLFV 15 2.786 MP03001 MAL3P2.11 36 100.0032 ELNYDNAGTNLYNEL 15 1.040 MP03001 MAL3P2.11 342 100.0033 QVRIKPGSANKPKDE 15 0.460 1369.t00001 Chromosome11 28 100.0034 LLKIWKNYMKIMNHL 15 0.328 1369.t00001 Chromosome11 43 100.0035 MTLYQIQVMKRNQKQ 15 0.056 1369.t00001 Chromosome11 57 100.0036 QKQVQMMIMIKFMGV 15 0.016 1369.t00001 Chromosome11 63 100.0037 MIMIKFMGVIYIMII 15 0.545 1369.t00001 Chromosome11 70 100.0038 GVIYIMIISKKMMRK 15 0.076 1369.t00001 Chromosome11 285 100.0039 LYYLFNQHIKKELYH 15 0.742 1369.t00001 Chromosome11 299 100.0040 HFNMLKNKMQSSFFM 15 0.560 1369.t00001 Chromosome11 353 100.0041 XDIYQKLYIKQEEQK 15 0.807 1369.t00001 Chromosome11 366 100.0042 QKKYIYNLIMNTQNK 15 0.167 1369.t00001 Chromosome11 381 100.0043 YEALIKLLPFSKRIR 15 0.701 699.t00001 Chromosome11 565 100.0044 NIHFAVLFLTLTVYP 15 0.347 699.t00001 Chromosome11 569 100.0045 AVLFLTLTVYPINNF 15 0.255 699.t00001 Chromosome11 623 100.0046 KLLYKMNYLKQDINN 15 0.545 699.t00001 Chromosome11 744 100.0047 KKEFKNSLILLNLYN 15 0.576 699.t00001 Chromosome11 773 100.0048 YLSFKILNTLLYNHI 15 0.234 699.t00001 Chromosome11 866 100.0049 IYILINHVIIPSLFY 15 0.400 699.t00001 Chromosome11 875 100.0050 IPSLFYLYMNFLKFI 15 0.347 699.t00001 Chromosome11 929 100.0051 KYLIILLYIFKLIEY 15 0.701 699.t00001 Chromosome11 978 100.0052 FIFMQNNQTKLAEMK 15 0.039 699.t00001 Chromosome11 1032 100.0053 LFIYIWLHLIIIFIF 15 0.423 mal_4T2c4.p1t1 15 100.0054 ILLIRPMLVKLRPKL 15 0.221 mal_4T2c4.p1t1 19 100.0055 RPMLVKLRPKLVKLR 15 0.083 mal_4T2c4.p1t1 26 100.0056 RPKLVKLRPMLVKLG 15 0.010 mal_4T2c4.p1t1 33 100.0057 RPMLVKLGPILVKLR 15 0.004 mal_4T2c4.p1t1 40 100.0058 GPILVKLRPMLVKLR 15 0.010 mal_4T2c4.p1t1 47 100.0059 RPMLVKLRPMLAKLR 15 0.016 mal_4T2c4.p1t1 54 100.0060 RPMLAKLRPMLAKLR 15 0.027 mal_4T2c4.p1t1 61 100.0061 RPMLAKLRPKLVKLR 15 0.137 mal_4T2c4.p1t1 68 100.0062 RPKLVKLRPKLVKLR 15 0.083 mal_4T2c4.p1t1 75 100.0063 RPKLVKLRPISVNAK 15 0.076 M13Hg2.q1t3 89 100.0064 ILEMKPNILLSRFIF 15 0.742 M13Hg2.q1t3 122 100.0065 NISINNAFSLPVNIY 15 0.663 M13Hg2.q1t3 163 100.0066 YFNIIQQKIQSNFLL 15 0.487 M13Hg2.q1t3 281 100.0067 ISTFIKNNINHQENN 15 0.682 M13Hg2.q1t3 442 100.0068 LKNMDGNILIKDFIQ 15 0.378 M13Hg2.q1t3 488 100.0069 IEFYNINMAKKVMNN 15 0.285 M13Hg2.q1t3 492 100.0070 NINMAKKVMNNMEKN 15 0.145 M13Hg2.q1t3 558 100.0071 FVNYFEAVVHMNIHC 15 0.831 M13Hg2.q1t3 691 100.0072 NNNIINGHMLEQKLS 15 0.123 M13Hg2.q1t3 869 100.0073 NNDMKKGYTNVSNNS 15 0.162 Mal_5L10c4.q1t6 154 100.0074 NNEFFGYPLQFVCET 15 0.255 Mal_5L10c4.q1t6 336 100.0075 FFIIKNVGVHKITYY 15 0.388 Mal_5L10c4.q1t6 1090 100.0076 KIEYISMLSPTINEI 15 0.113 Mal_5L10c4.q1t6 1101 100.0077 INEIKTLNTILTIPL 15 0.018 Mal_5L10c4.q1t6 1107 100.0078 LNTILTIPLIKMNEY 15 0.042 Mal_5L10c4.q1t6 1264 100.0079 HKLFINKLMTSNIRK 15 0.203 Mal_5L10c4.q1t6 1289 100.0080 QNRFRNQLLYLTKIA 15 0.050 Mal_5L10c4.q1t6 1609 100.0081 IKKIKTPLILPIDPN 15 0.035 Mal_5L10c4.q1t6 1888 100.0082 QDHLVIQIIYVMDNI 15 0.133 Mal_5L10c4.q1t6 2031 100.0083 IEAMGGAHSIGYEQF 15 0.068 571.t00003 Chromosome11 33 100.0084 FDDFKINYSYKTKNH 15 0.182 571.t00003 Chromosome11 462 100.0085 ITDLNNMNVNQSNMK 15 0.500 571.t00003 Chromosome11 960 100.0086 TNNFNNNVMMLMNTS 15 0.007 571.t00003 Chromosome11 1124 100.0087 EQNVAQNVAQNVAQN 15 0.460 571.t00003 Chromosome11 1128 100.0088 AQNVAQNVAQNVEQN 15 0.460 571.t00003 Chromosome11 1550 100.0089 SNKFMTPTTLKEKYQ 15 0.255 571.t00003 Chromosome11 1941 100.0090 NIHMINDVATKLNQH 15 0.285 571.t00003 Chromosome11 2112 100.0091 HIHMMNQQIQKETNT 15 0.576 571.t00003 Chromosome11 2255 100.0092 NNVFQQPLSYSNGSE 15 0.347 571.t00003 Chromosome11 2738 100.0093 NNTINMNGMNKTESI 15 0.198 MP03072 PFC0450w 5 100.0094 LNILILIDAASVAFL 15 0.722 MP03072 PFC0450w 8 100.0095 LILIDAASVAFLLIT 15 1.340 MP03072 PFC0450w 17 100.0096 AFLLITFLMINLNEE 15 1.197 MP03072 PFC0450w 44 100.0097 KKALVVAIILYVIFL 15 0.302 MP03072 PFC0450w 48 100.0098 VVAIILYVIFLVLLF 15 0.609 MP03072 PFC0450w 52 100.0099 ILYVIFLVLLFIYKA 15 0.831 MP03072 PFC0450w 55 100.0100 VIFLVLLFIYKAYKN 15 0.956 MP03072 PFC0450w 58 100.0101 LVLLFIYKAYKNKRK 15 4.016 MP03072 PFC0450w 76 100.0102 NFFMKKRNAPKYVQL 15 0.593 MP03072 PFC0450w 85 100.0103 PKYVQLASTYLSASD 15 2.865 45.t00001 Chromosome14 2 100.0104 ENEYATGAVRPFQAA 15 0.722 45.t00001 Chromosome14 27 100.0105 NYELSKKAVIFTPIY 15 1.197 45.t00001 Chromosome14 108 100.0106 QKILIKIPVTKNIIT 15 0.085 45.t00001 Chromosome14 156 100.0107 KCLVISQVSNSDSYK 15 2.044 45.t00001 Chromosome14 202 100.0108 SKIMKLPKLPISNGK 15 0.742 45.t00001 Chromosome14 220 100.0109 FIHFFTWGTMFVPKY 15 0.026 45.t00001 Chromosome14 242 100.0110 LCNFKKNIIALLIIP 15 0.203 45.t00001 Chromosome14 246 100.0111 KKNIIALLIIPPKIH 15 0.010 45.t00001 Chromosome14 251 100.0112 ALLIIPPKIHISIEL 15 1.267 45.t00001 Chromosome14 274 100.0113 SMEYKKDFLITARKP 15 1.826 MP03137 PFC0700c 7 100.0114 KSKFNILSSPLFNNF 15 1.987 MP03137 PFC0700c 173 100.0115 FKKLKNHVLFLQMMN 15 0.785 MP03137 PFC0700c 177 100.0116 KNHVLFLQMMNVNLQ 15 0.095 MP03137 PFC0700c 180 100.0117 VLFLQMMNVNLQKQL 15 0.068 MP03137 PFC0700c 187 100.0118 NVNLQKQLLTNHLIN 15 0.956 MP03137 PFC0700c 191 100.0119 QKQLLTNHLINTPKI 15 1.132 MP03137 PFC0700c 197 100.0120 NHLINTPKIMPHHII 15 0.576 MP03137 PFC0700c 239 100.0121 YILLKKILSSRFNQM 15 1.100 MP03137 PFC0700c 250 100.0122 FNQMIFVSSIFISFY 15 2.420 12.t00018 Chromosome14 36 100.0123 CNILKENNTYKQKKH 15 4.016 12.t00018 Chromosome14 133 100.0124 TNELKKMDTKKDVHM 15 1.011 12.t00018 Chromosome14 504 100.0125 EVKFILHMTLLTLYK 15 0.269 12.t00018 Chromosome14 542 100.0126 KYNFLNIYASLRNEY 15 0.328 12.t00018 Chromosome14 583 100.0127 TRCFKNSYPKKVWKK 15 0.293 12.t00018 Chromosome14 612 100.0128 NNLYVSMYIPFIKKF 15 0.411 12.t00018 Chromosome14 1000 100.0129 EAKFKIERLLKSSYK 15 3.298 12.t00018 Chromosome14 1057 100.0130 KIYILNNNLLIVHLS 15 1.543 12.t00018 Chromosome14 1184 100.0131 KCSFDKTNPIQQSGK 15 2.044 12.t00018 Chromosome14 1212 100.0132 TGIFNMPNLVQINNY 15 0.078 mal_BU121g9.q1c1 29 100.0133 EGMLTVAGPRSQTEL 15 3.298 mal_9A57b11.q1t2 3 100.0134 KQNIKYTQIISIDNI 15 2.633 mal_9A57b11.q1t2 18 100.0135 LNKIADPILIGFSSS 15 0.929 mal_9A57b11.q1t2 123 100.0136 NRIYNKLKLHKIIRK 15 1.267 mal_9A57b11.q1t2 194 100.0137 NNEYGILNAQKALSN 15 0.098 mal_9A57b11.q1t2 197 100.0138 YGILNAQKALSNLHK 15 0.141 mal_9A57b11.q1t2 229 100.0139 KIFVKYLPLFLMMEH 15 0.042 mal_9A57b11.q1t2 236 100.0140 PLFLMMEHSFLNCHK 15 3.031 mal_BL50e8.p1ca_5 1 100.0141 MEGFVALLSFLVVLV 15 0.004 mal_BL50e8.p1ca_5 100 100.0142 VDGMKIGHPISVALG 15 0.010 mal_BL50e8.p1ca_5 151 100.0143 GSTYMTPSAIKIKVP 15 0.057 mal_BL50e8.p1ca_5 189 100.0144 NNLFIYNWVLQTSSP 15 0.560 mal_BL50e8.p1ca_5 347 100.0145 EKILIRALLSLDFSL 15 0.722 mal_BL50e8.p1ca_5 437 100.0146 HPVYPTAPAVAFPAG 15 0.187 mal_BL50e8.p1ca_5 585 100.0147 EVYYFPGKVTRVRAK 15 0.357 mal_BL50e8.p1ca_5 606 100.0148 EDKLVKIYISLLSSD 15 0.423 mal_BL50e8.p1ca_5 685 100.0149 IERYVGLGSFHFYLY 15 0.423 mal_BL50e8.p1ca_5 816 100.0150 CFQVLNPVTIPKYCI 15 0.285 M13S8h6.p1t_3 68 100.0151 FMSFKILEALLVCIS 15 0.006 M13S8h6.p1t_3 127 100.0152 KQIVIFLISLLSFTL 15 0.473 M13S8h6.p1t_3 169 100.0153 AKQIEILHTMLPNFL 15 0.095 M13S8h6.p1t_3 218 100.0154 IDDFQNMVSTLQPHV 15 0.034 M13S8h6.p1t_3 285 100.0155 KCAIKLAIAQLSAKY 15 0.130 M13S8h6.p1t_3 343 100.0156 IGSVKPQYALFGDTV 15 0.228 M13S8h6.p1t_3 871 100.0157 KIYIKKKRLLQMNNY 15 0.411 M13S8h6.p1t_3 1350 100.0158 KKLLKKLTSNLQLNK 15 0.076 M13S8h6.p1t_3 1602 100.0159 QDFLTKILPRQVLEE 15 0.241 M13S8h6.p1t_3 1754 100.0160 MWGLDVLIANKIESN 15 0.423 585.t00002 Chromosome11 5 100.0161 FFILFYFYVMSTYTF 15 0.500 585.t00002 Chromosome11 16 100.0162 TYTFCFLPVLQTQLG 15 0.515 585.t00002 Chromosome11 349 100.0163 KKKYKNKKMPKTIDG 15 0.473 585.t00002 Chromosome11 487 100.0164 GRAIIPLFLILNTYK 15 0.269 585.t00002 Chromosome11 562 100.0165 KIIFKRNPLFLTFLS 15 0.367 585.t00002 Chromosome11 643 100.0166 WLFFFDLVVLSPFSL 15 0.500 585.t00002 Chromosome11 774 100.0167 KNIIKGKNMMTRGGG 15 0.106 585.t00002 Chromosome11 796 100.0168 KMFIKGDTVMKANII 15 0.038 585.t00002 Chromosome11 1093 100.0169 VGSYKLMISQEAEFE 15 0.487 585.t00002 Chromosome11 1344 100.0170 LNRFITLITWTQHVS 15 0.095 1223.t00015 mal_9A21f9.q1t_4 1070 100.0171 RTKYETLVTIHVHQR 15 0.087 1223.t00015 mal_9A21f9.q1t_4 1162 100.0172 GLCYGGAPAGPAGTG 15 0.059 1223.t00015 mal_9A21f9.q1t_4 1654 100.0173 DSILILQTINLLNSQ 15 0.177 1223.t00015 mal_9A21f9.q1t_4 2461 100.0174 KHLIIINRVMQTPNG 15 0.043 1223.t00015 mal_9A21f9.q1t_4 2779 100.0175 IDLYKQMYVKKYDEI 15 0.158 1223.t00015 mal_9A21f9.q1t_4 2878 100.0176 DKDLKAALPYLHEAE 15 0.103 1223.t00015 mal_9A21f9.q1t_4 2985 100.0177 TIELLKPYIQSTFFK 15 0.145 1223.t00015 mal_9A21f9.q1t_4 2995 100.0178 STFFKTQIAKKASVA 15 0.002 1223.t00015 mal_9A21f9.q1t_4 3014 100.0179 CKWVGAMAMYNQASK 15 0.145 1223.t00015 mal_9A21f9.q1t_4 3019 100.0180 AMAMYNQASKIVKPK 15 0.116 599.t00001 Chromosome11 12 100.0181 INFFILLTLVFQKYS 15 0.177 599.t00001 Chromosome11 364 100.0182 NNNLGIPTLIKKEVH 15 0.234 599.t00001 Chromosome11 519 100.0183 EEDIKNAYLPENKNF 15 0.435 599.t00001 Chromosome11 1074 100.0184 INVFIKEISKLFDHD 15 0.529 599.t00001 Chromosome11 1414 100.0185 DKSLKIMYSLFNKYT 15 0.098 599.t00001 Chromosome11 1463 100.0186 VVIFIYGNIIISDLK 15 0.645 599.t00001 Chromosome11 1621 100.0187 CESFISKVTNKVIKK 15 0.215 599.t00001 Chromosome11 1740 100.0188 ICTFVKYITFQLLNI 15 0.854 599.t00001 Chromosome11 1767 100.0189 KEHYIMNNTIFTFNQ 15 0.141 599.t00001 Chromosome11 1892 100.0190 KKKYKYIPSNGTTQS 15 0.500 M1045c5.p1c.C_6 53 100.0191 EKSLGILGSIQNAYL 15 0.085 M1045c5.p1c.C_6 59 100.0192 LGSIQNAYLYKSIFK 15 0.388 M1045c5.p1c.C_6 588 100.0193 SCIMNNMIVTKESNE 15 0.473 M1045c5.p1c.C_6 1040 100.0194 KDFMKNNTTLFSHFN 15 0.241 M1045c5.p1c.C_6 1136 100.0195 MLYLIRNILMSIEDY 15 0.435 M1045c5.p1c.C_6 1229 100.0196 KKKYIKLNIFKNIIL 15 0.378 M1045c5.p1c.C_6 1350 100.0197 RWDLVMNMMIGIRIS 15 0.054 M1045c5.p1c.C_6 1380 100.0198 HKDVIQLPTSNAQHK 15 0.167 M1045c5.p1c.C_6 1393 100.0199 HKVIFKNYAPIIFKN 15 0.262 M1045c5.p1c.C_6 1430 100.0200 SNMVLGNLSTLSELL 15 0.423 PIR2 T28161 46 100.0201 AKFYNGGEIMQPNSK 15 0.153 PIR2 T28161 319 100.0202 KRNLKLQNAIKNCRG 15 0.043 PIR2 T28161 1072 100.0203 HVKIIKNLLIHGKEQ 15 0.302 PIR2 T28161 1093 100.0204 KYKLLYLQAQTTAAN 15 0.141 PIR2 T28161 1096 100.0205 LLYLQAQTTAANGGP 15 0.047 PIR2 T28161 1589 100.0206 SPKIVVPAPKPTTTF 15 0.119 PIR2 T28161 1951 100.0207 FVDLIRQIAATIDKG 15 0.047 PIR2 T28161 2065 100.0208 QERLVKNPLVQPTLK 15 0.028 PIR2 T28161 2129 100.0209 HPAVIPALVTSTLAW 15 0.072 PIR2 T28161 2419 100.0210 NELFGTNHVKQTSIH 15 0.098 55.t00004 Chromosome14 81 100.0211 NNEFVVAQLYELNNY 15 1.340 55.t00004 Chromosome14 117 100.0212 DNNMKKYLIQKCGKK 15 1.776 55.t00004 Chromosome14 218 100.0213 SCSIIKYELRKTSIC 15 1.878 55.t00004 Chromosome14 385 100.0214 RNHMDKPPPHNINNN 15 0.228 55.t00004 Chromosome14 613 100.0215 NNNLIFQNSRFMDHT 15 0.423 55.t00004 Chromosome14 754 100.0216 THDIIKNVSNNMKRF 15 0.357 55.t00004 Chromosome14 904 100.0217 FKNVDMLNIYKINKD 15 1.987 55.t00004 Chromosome14 1136 100.0218 MKDVINLYTYVVNKK 15 0.092 55.t00004 Chromosome14 1364 100.0219 GMYILPQYVTRECIN 15 1.500 55.t00004 Chromosome14 1510 100.0220 GDDVIYEETKKTDNI 15 1.587 13.t00011 Chromosome14 16 100.0221 FKSLKNNNMLESTGI 15 1.587 13.t00011 Chromosome14 49 100.0222 FLDYVKGKMMDVYKE 15 0.126 13.t00011 Chromosome14 84 100.0223 TYNYLTPTLKVKRFR 15 3.589 37.t00002 Chromosome14 50 100.0224 NDLIDQNIVYLNVCN 15 2.560 674.t00001 Chromosome11 30 100.0225 LKKLKKILLNLDVLI 15 0.742 674.t00001 Chromosome11 54 100.0226 NENFDMELLNNVNDR 15 1.378 674.t00001 Chromosome11 124 100.0227 NCPIKNEVTTLIQKI 15 0.367 674.t00001 Chromosome11 296 100.0228 EKNMTSQKSITSEKN 15 0.854 674.t00001 Chromosome11 577 100.0229 NSNFKEQHLLFCNNL 15 1.418 674.t00001 Chromosome11 752 100.0230 NNNIKTHIANFNIIH 15 1.040 674.t00001 Chromosome11 986 100.0231 NNLYKTYEMIQGDND 15 0.956 674.t00001 Chromosome11 1093 100.0232 NDNYINNNIYLNKAN 15 1.340 674.t00001 Chromosome11 1353 100.0233 FLQYRIPHMNNNGNI 15 0.983 674.t00001 Chromosome11 1432 100.0234 VDIFCKIHALKNENK 15 0.854 

1-29. (canceled)
 30. A composition of matter comprising: a) an isolated, purified or isolated and purified polynucleotide sequence comprising: 1) a polynucleotide sequence encoding: i) a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 2) a complementary polynucleotide sequence to: i) a polynucleotide sequence encoding a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polynucleotide sequence encoding a polypeptide sequence as set forth in Tables 2, 3, 4, 5, or 6; 3) a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence of (1) or (2); 4) a fragment of a polynucleotide sequence according to (1) or (2); 5) a polynucleotide sequence encoding a variant of: i) a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 6) a polynucleotide sequence encoding a polypeptide fragment of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment has substantially the same serologic reactivity as the native polypeptide and substantially the same T-cell reactivity as the native polypeptide or fragment; 7) a polynucleotide sequence encoding a fragment of a variant polypeptide of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment of the variant polypeptide has substantially the same serologic activity as the native polypeptide or substantially the same T-cell reactivity as the native polypeptide or fragment; 8) a polynucleotide sequence encoding a multi-epitope construct; 9) a primer or detection probe for hybridization with a target sequence or the amplicon generated from a target sequence comprising a sequence of at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 consecutive nucleotides of the polynucleotide sequences according to (1), (2), (3), (4), (5), (6), (7), or (8); or 10) a polynucleotide sequence according to (1), (2), (3), (4), (5), (6), (7), or (8) that further comprises regulatory sequences; b) a DNA chip comprising: 1) a polynucleotide sequence encoding: i) a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 2) a complementary polynucleotide sequence to: i) a polynucleotide sequence encoding a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polynucleotide sequence encoding a polypeptide sequence as set forth in Tables 2, 3, 4, 5, or 6; 3) a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence of (1) or (2); 4) a fragment of a polynucleotide sequence according to (1) or (2); 5) a polynucleotide sequence encoding a variant of: i) a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 6) a polynucleotide sequence encoding a polypeptide fragment of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment has substantially the same serologic reactivity as the native polypeptide and substantially the same T-cell reactivity as the native polypeptide or fragment; 7) a polynucleotide sequence encoding a fragment of a variant polypeptide of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment of the variant polypeptide has substantially the same serologic activity as the native polypeptide or substantially the same T-cell reactivity as the native polypeptide or fragment; 8) a polynucleotide sequence encoding a multi-epitope construct; or 9) a primer or detection probe for hybridization with a target sequence or the amplicon generated from a target sequence comprising a sequence of at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 consecutive nucleotides of the polynucleotide sequences according to (1), (2), (3), (4), (5), (6), (7), or (8); c) a vector comprising a promoter operably linked to a nucleic acid sequence comprising: 1) a polynucleotide sequence encoding: i) a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 2) a complementary polynucleotide sequence to: i) a polynucleotide sequence encoding a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polynucleotide sequence encoding a polypeptide sequence as set forth in Tables 2, 3, 4, 5, or 6; 3) a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence of (1) or (2); 4) a fragment of a polynucleotide sequence according to (1) or (2); 5) a polynucleotide sequence encoding a variant of: i) a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 6) a polynucleotide sequence encoding a polypeptide fragment of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment has substantially the same serologic reactivity as the native polypeptide and substantially the same T-cell reactivity as the native polypeptide or fragment; 7) a polynucleotide sequence encoding a fragment of a variant polypeptide of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment of the variant polypeptide has substantially the same serologic activity as the native polypeptide or substantially the same T-cell reactivity as the native polypeptide or fragment; 8) a polynucleotide sequence encoding a multi-epitope construct; or 9) a primer or detection probe for hybridization with a target sequence or the amplicon generated from a target sequence comprising a sequence of at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 consecutive nucleotides of the polynucleotide sequences according to (1), (2), (3), (4), (5), (6), (7), or (8); d) a host cell comprising: 1) a vector according to (c); or 2) an isolated, purified or isolated and purified polynucleotide according to (a); or e) an isolated polypeptide comprising: 1) SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27; 2) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 3) a fragment of a polypeptide or a variant polypeptide of: a) a polypeptide set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27; or b) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6, wherein said fragment or variant has substantially the same serologic reactivity or substantially the same T-cell reactivity as the native polypeptide; 4) a variant polypeptide having at least about 20% to 99.99% identity to a polypeptide provided in Table 2, 3, 4, 5, or 6 or selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; 5) a polypeptide epitope as set forth in Table 2, 3, 4, 5, or 6; or 6) a multi-epitope construct: i) comprising at least one epitope set forth in Table 2, 3, 4, 5, or 6; ii) comprising a polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27 and at least one epitope set forth in Table 2, 3, 4, 5, or 6; or iii) comprising and at least one epitope set forth in Table 2, 3, 4, 5, or 6 and one or more polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or f) an isolated antibody that specifically binds an isolated polypeptide comprising: 1) SEQ ID NO:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27; 2) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 3) a fragment of a polypeptide or a variant polypeptide of: a) a polypeptide set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27; or b) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6, wherein said fragment or variant has substantially the same serologic reactivity or substantially the same T-cell reactivity as the native polypeptide; 4) a variant polypeptide having at least about 20% to 99.99% identity to a polypeptide provided in Table 2, 3, 4, 5, or 6 or selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; 5) a polypeptide epitope as set forth in Table 2, 3, 4, 5, or 6; or 6) a multi-epitope construct: i) comprising at least one epitope set forth in Table 2, 3, 4, 5, or 6; ii) comprising a polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27 and at least one epitope set forth in Table 2, 3, 4, 5, or 6; or iii) comprising and at least one epitope set forth in Table 2, 3, 4, 5, or 6 and one or more polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and
 27. 31. The composition of matter according to claim 30, wherein said polynucleotide further comprises a label.
 32. The composition of matter according to claim 31, wherein said label is a: 1) radioactive label, 2) enzyme label, 3) chemiluminescent label, 4) fluorescent label, or 5) magnetic label.
 33. The composition of matter according to claim 30, wherein said regulatory sequences are promoters, enhancer elements, or termination sequences that are operably linked to a polynucleotide.
 34. The composition of matter according to claim 30, wherein said vector comprises a promoter operably linked to a nucleic acid sequence.
 35. The composition of matter according to claim 34, wherein said vector contains one or more origins of replication.
 36. The composition of matter according to claim 35, wherein said vector contains one or more selectable markers.
 37. The composition of matter according to claim 34, wherein said vector contains one or more selectable markers.
 38. The composition of matter according to claim 34 vector according to claim 9, wherein said vector is a vaccine vector or a viral vector.
 39. The composition of matter according to claim 30, wherein said composition of matter further comprises a pharmaceutically acceptable carrier.
 40. The composition of matter according to claim 39, wherein said carrier is an adjuvant.
 41. The composition of matter according to claim 30, wherein the polypeptide epitope is a CTL-inducing peptide epitope or a HTL-inducing peptide epitope.
 42. The composition of matter according to claim 30, wherein said antibody binds an epitope that a CTL-inducing peptide epitope or a HTL-inducing peptide epitope.
 43. A method of inducing an immune response in an individual comprising the administration of a composition of matter to an individual in an amount sufficient to induce an immune response, wherein said composition of matter is: a) an isolated, purified or isolated and purified polynucleotide sequence comprising: 1) a polynucleotide sequence encoding: i) a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 2) a complementary polynucleotide sequence to: i) a polynucleotide sequence encoding a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polynucleotide sequence encoding a polypeptide sequence as set forth in Tables 2, 3, 4, 5, or 6; 3) a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence of (1) or (2); 4) a fragment of a polynucleotide sequence according to (1) or (2); 5) a polynucleotide sequence encoding a variant of: i) a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 6) a polynucleotide sequence encoding a polypeptide fragment of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment has substantially the same serologic reactivity as the native polypeptide and substantially the same T-cell reactivity as the native polypeptide or fragment; 7) a polynucleotide sequence encoding a fragment of a variant polypeptide of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment of the variant polypeptide has substantially the same serologic activity as the native polypeptide or substantially the same T-cell reactivity as the native polypeptide or fragment; or 8) a polynucleotide sequence encoding a multi-epitope construct; or b) an isolated polypeptide comprising: 1) SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27; 2) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 3) a fragment of a polypeptide or a variant polypeptide of: a) a polypeptide set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27; or b) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6, wherein said fragment or variant has substantially the same serologic reactivity or substantially the same T-cell reactivity as the native polypeptide; 4) a variant polypeptide having at least about 20% to 99.99% identity to a polypeptide provided in Table 2, 3, 4, 5, or 6 or selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; 5) a polypeptide epitope as set forth in Table 2, 3, 4, 5, or 6; or 6) a multi-epitope construct: i) comprising at least one epitope set forth in Table 2, 3, 4, 5, or 6; ii) comprising a polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27 and at least one epitope set forth in Table 2, 3, 4, 5, or 6; or iii) comprising and at least one epitope set forth in Table 2, 3, 4, 5, or 6 and one or more polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and
 27. 44. A method of detecting a P. falciparum antigen comprising contacting a biological sample obtained from an individual with: a) an isolated, purified or isolated and purified polynucleotide sequence comprising: 1) a polynucleotide sequence encoding: i) a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 2) a complementary polynucleotide sequence to: i) a polynucleotide sequence encoding a polypeptide sequence selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polynucleotide sequence encoding a polypeptide sequence as set forth in Tables 2, 3, 4, 5, or 6; 3) a polynucleotide sequence having at least about 20% to 99.99% identity to a polynucleotide sequence of (1) or (2); 4) a fragment of a polynucleotide sequence according to (1) or (2); 5) a polynucleotide sequence encoding a variant of: i) a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; or ii) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 6) a polynucleotide sequence encoding a polypeptide fragment of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment has substantially the same serologic reactivity as the native polypeptide and substantially the same T-cell reactivity as the native polypeptide or fragment; 7) a polynucleotide sequence encoding a fragment of a variant polypeptide of a polypeptide selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment of the variant polypeptide has substantially the same serologic activity as the native polypeptide or substantially the same T-cell reactivity as the native polypeptide or fragment; or 8) a polynucleotide sequence encoding a multi-epitope construct; or b) an isolated polypeptide comprising: 1) SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27; 2) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6; 3) a fragment of a polypeptide or a variant polypeptide of: a) a polypeptide set forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27; or b) a polypeptide as set forth in Tables 2, 3, 4, 5, or 6, wherein said fragment or variant has substantially the same serologic reactivity or substantially the same T-cell reactivity as the native polypeptide; 4) a variant polypeptide having at least about 20% to 99.99% identity to a polypeptide provided in Table 2, 3, 4, 5, or 6 or selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; 5) a polypeptide epitope as set forth in Table 2, 3, 4, 5, or 6; or 6) a multi-epitope construct: i) comprising at least one epitope set forth in Table 2, 3, 4, 5, or 6; ii) comprising a polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27 and at least one epitope set forth in Table 2, 3, 4, 5, or 6; or iii) comprising and at least one epitope set forth in Table 2, 3, 4, 5, or 6 and one or more polypeptide selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; and detecting the formation of a nucleic acid hybrid or an antigen-antibody complex. 